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HEADER SIGNALING PROTEIN 29-JUL-10 2XMQ
TITLE CRYSTAL STRUCTURE OF HUMAN NDRG2 PROTEIN PROVIDES INSIGHT INTO ITS
TITLE 2 ROLE AS A TUMOR SUPPRESSOR
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROTEIN NDRG2;
COMPND 3 CHAIN: A, B, C;
COMPND 4 FRAGMENT: ALPHA-BETA HYDROLASE DOMAIN, RESIDUES 24-304;
COMPND 5 SYNONYM: NDRG2;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS SIGNALING PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR J.HWANG,Y.KIM,H.LEE,M.H.KIM
REVDAT 1 19-JAN-11 2XMQ 0
JRNL AUTH J.HWANG,Y.KIM,H.LEE,M.H.KIM
JRNL TITL CRYSTAL STRUCTURE OF HUMAN NDRG2 PROTEIN PROVIDES INSIGHT
JRNL TITL 2 INTO ITS ROLE AS A TUMOR SUPPRESSOR
JRNL REF J.BIOL.CHEM. 2011
JRNL REFN ESSN 1083-351X
REMARK 2
REMARK 2 RESOLUTION. 2.81 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0019
REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.81
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.19
REMARK 3 NUMBER OF REFLECTIONS : 23070
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.20390
REMARK 3 R VALUE (WORKING SET) : 0.20095
REMARK 3 FREE R VALUE : 0.25847
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1
REMARK 3 FREE R VALUE TEST SET COUNT : 1242
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.807
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.880
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1572
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.38
REMARK 3 BIN R VALUE (WORKING SET) : 0.279
REMARK 3 BIN FREE R VALUE SET COUNT : 92
REMARK 3 BIN FREE R VALUE : 0.346
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 6615
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 12
REMARK 3 SOLVENT ATOMS : 93
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 0
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.372
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.11
REMARK 3 B22 (A**2) : -1.11
REMARK 3 B33 (A**2) : 1.22
REMARK 3 B12 (A**2) : 0.00
REMARK 3 B13 (A**2) : 0.00
REMARK 3 B23 (A**2) : 0.00
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.400
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.297
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.182
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.885
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6798 ; 0.029 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9255 ; 2.332 ; 1.961
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 840 ; 9.456 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 318 ;40.244 ;25.000
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1083 ;21.222 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;25.877 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1005 ; 0.137 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5286 ; 0.008 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3047 ; 0.260 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4727 ; 0.338 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 227 ; 0.186 ; 0.200
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 60 ; 0.324 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.316 ; 0.200
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 4290 ; 1.114 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6807 ; 1.833 ; 2.000
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2820 ; 2.371 ; 3.000
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2448 ; 3.501 ; 4.500
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 3
REMARK 3
REMARK 3 NCS GROUP NUMBER : 1
REMARK 3 CHAIN NAMES : A B
REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1
REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE
REMARK 3 1 A 24 A 304 1
REMARK 3 1 B 24 B 304 1
REMARK 3 GROUP CHAIN COUNT RMS WEIGHT
REMARK 3 TIGHT POSITIONAL 1 A (A): 2205 ; 0.14 ; 0.05
REMARK 3 TIGHT POSITIONAL 1 B (A): 2205 ; 0.14 ; 0.05
REMARK 3 TIGHT THERMAL 1 A (A**2): 2205 ; 0.18 ; 0.50
REMARK 3 TIGHT THERMAL 1 B (A**2): 2205 ; 0.18 ; 0.50
REMARK 3
REMARK 3 NCS GROUP NUMBER : 2
REMARK 3 CHAIN NAMES : B C
REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1
REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE
REMARK 3 1 B 24 B 304 1
REMARK 3 1 C 24 C 304 1
REMARK 3 GROUP CHAIN COUNT RMS WEIGHT
REMARK 3 TIGHT POSITIONAL 2 B (A): 2205 ; 0.13 ; 0.05
REMARK 3 TIGHT POSITIONAL 2 C (A): 2205 ; 0.13 ; 0.05
REMARK 3 TIGHT THERMAL 2 B (A**2): 2205 ; 0.21 ; 0.50
REMARK 3 TIGHT THERMAL 2 C (A**2): 2205 ; 0.21 ; 0.50
REMARK 3
REMARK 3 NCS GROUP NUMBER : 3
REMARK 3 CHAIN NAMES : C A
REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1
REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE
REMARK 3 1 C 24 C 304 1
REMARK 3 1 A 24 A 304 1
REMARK 3 GROUP CHAIN COUNT RMS WEIGHT
REMARK 3 TIGHT POSITIONAL 3 C (A): 2205 ; 0.15 ; 0.05
REMARK 3 TIGHT POSITIONAL 3 A (A): 2205 ; 0.15 ; 0.05
REMARK 3 TIGHT THERMAL 3 C (A**2): 2205 ; 0.19 ; 0.50
REMARK 3 TIGHT THERMAL 3 A (A**2): 2205 ; 0.19 ; 0.50
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS.
REMARK 4
REMARK 4 2XMQ COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-JUL-10.
REMARK 100 THE PDBE ID CODE IS EBI-44852.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : PAL/PLS
REMARK 200 BEAMLINE : 4A
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : NULL
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24361
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.81
REMARK 200 RESOLUTION RANGE LOW (A) : 40.00
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6
REMARK 200 DATA REDUNDANCY : 6.6
REMARK 200 R MERGE (I) : 0.10
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 19.10
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0
REMARK 200 DATA REDUNDANCY IN SHELL : 6.3
REMARK 200 R MERGE FOR SHELL (I) : 0.42
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : 4.50
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: PDB ENTRY 2QMQ
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 55
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.7
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 9% PEG 8000, 0.2 M CALCIUM ACETATE, 0.1
REMARK 280 M SODIUM CACODYLATE (PH 6.4 TO 7.5).
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 X+1/2,-Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 43.20550
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.39950
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.44850
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.39950
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.20550
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.44850
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2, 3
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 3
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: C
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
REMARK 500 GLU A 30 CD GLU A 30 OE1 0.083
REMARK 500 GLU A 30 CD GLU A 30 OE2 0.094
REMARK 500 GLN A 103 CB GLN A 103 CG -0.236
REMARK 500 TYR A 120 CG TYR A 120 CD2 -0.106
REMARK 500 TYR A 120 CG TYR A 120 CD1 -0.109
REMARK 500 TYR A 120 CE1 TYR A 120 CZ -0.128
REMARK 500 TYR A 120 CZ TYR A 120 CE2 -0.130
REMARK 500 ALA A 168 CA ALA A 168 CB -0.132
REMARK 500 GLU A 181 CB GLU A 181 CG 0.129
REMARK 500 GLN A 268 CD GLN A 268 OE1 -0.133
REMARK 500 GLU B 30 CG GLU B 30 CD -0.101
REMARK 500 GLU B 76 CG GLU B 76 CD 0.095
REMARK 500 TYR B 120 CG TYR B 120 CD2 -0.085
REMARK 500 TYR B 120 CG TYR B 120 CD1 -0.085
REMARK 500 TYR B 120 CZ TYR B 120 CE2 -0.089
REMARK 500 GLU B 181 CD GLU B 181 OE2 -0.083
REMARK 500 GLU B 191 CG GLU B 191 CD 0.122
REMARK 500 LYS C 62 CD LYS C 62 CE 0.151
REMARK 500 ARG C 204 CZ ARG C 204 NH1 -0.106
REMARK 500 ASN C 212 CB ASN C 212 CG -0.170
REMARK 500 ASN C 212 CG ASN C 212 OD1 -0.158
REMARK 500 GLN C 250 CG GLN C 250 CD 0.147
REMARK 500 CYS C 260 CB CYS C 260 SG -0.106
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 GLU A 30 CA - CB - CG ANGL. DEV. = -14.3 DEGREES
REMARK 500 GLU A 30 OE1 - CD - OE2 ANGL. DEV. = 7.4 DEGREES
REMARK 500 VAL A 82 CB - CA - C ANGL. DEV. = -11.7 DEGREES
REMARK 500 GLN A 103 N - CA - CB ANGL. DEV. = -14.6 DEGREES
REMARK 500 ARG A 140 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES
REMARK 500 ARG A 227 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES
REMARK 500 GLN A 285 CA - CB - CG ANGL. DEV. = -17.9 DEGREES
REMARK 500 GLU B 30 CA - CB - CG ANGL. DEV. = -16.5 DEGREES
REMARK 500 PRO B 44 C - N - CA ANGL. DEV. = -10.2 DEGREES
REMARK 500 GLU B 181 OE1 - CD - OE2 ANGL. DEV. = -8.9 DEGREES
REMARK 500 GLU B 181 CG - CD - OE1 ANGL. DEV. = 13.9 DEGREES
REMARK 500 ARG B 204 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES
REMARK 500 ARG B 204 NE - CZ - NH2 ANGL. DEV. = 5.1 DEGREES
REMARK 500 GLU C 30 CA - CB - CG ANGL. DEV. = -14.1 DEGREES
REMARK 500 GLU C 181 OE1 - CD - OE2 ANGL. DEV. = -8.1 DEGREES
REMARK 500 MET C 182 CB - CG - SD ANGL. DEV. = 24.8 DEGREES
REMARK 500 MET C 182 CG - SD - CE ANGL. DEV. = -12.4 DEGREES
REMARK 500 ARG C 204 NE - CZ - NH2 ANGL. DEV. = 6.9 DEGREES
REMARK 500 ASN C 212 N - CA - CB ANGL. DEV. = -14.5 DEGREES
REMARK 500 ASN C 212 CB - CG - OD1 ANGL. DEV. = -13.5 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 PRO A 32 -8.61 -59.56
REMARK 500 HIS A 145 58.44 -147.90
REMARK 500 THR A 176 -16.89 -142.91
REMARK 500 ASP A 265 108.92 -51.94
REMARK 500 GLN A 280 76.63 -119.73
REMARK 500 ALA B 133 -37.89 -39.33
REMARK 500 SER B 197 -179.18 -57.19
REMARK 500 VAL B 247 144.84 -176.27
REMARK 500 ASP B 265 105.57 -53.32
REMARK 500 GLN B 280 74.55 -116.57
REMARK 500 GLN B 285 55.55 -114.22
REMARK 500 PRO C 44 177.10 -58.23
REMARK 500 GLN C 79 -26.50 -36.35
REMARK 500 SER C 197 -178.16 -62.36
REMARK 500 ASP C 265 107.13 -57.49
REMARK 500 GLN C 285 56.76 -115.32
REMARK 500 MET C 303 108.66 -54.32
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 ARG B 233 GLY B 234 -63.95
REMARK 500 PRO C 44 LYS C 45 117.35
REMARK 500 GLN C 79 ASN C 80 -130.00
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CHIRAL CENTERS
REMARK 500
REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL
REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY
REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR
REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE
REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16)
REMARK 500
REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS
REMARK 500 PHE C 69 24.6 L L OUTSIDE RANGE
REMARK 500 GLN C 79 23.0 L L OUTSIDE RANGE
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B1305
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A1305
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C1305
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2XMR RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN NDRG2 PROTEIN PROVIDES INSIGHT
REMARK 900 INTO ITS ROLE AS A TUMOR SUPPRESSOR
REMARK 900 RELATED ID: 2XMS RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN NDRG2 PROTEIN PROVIDES INSIGHT
REMARK 900 INTO ITS ROLE AS A TUMOR SUPPRESSOR
DBREF 2XMQ A 24 304 UNP Q9UN36 NDRG2_HUMAN 24 304
DBREF 2XMQ B 24 304 UNP Q9UN36 NDRG2_HUMAN 24 304
DBREF 2XMQ C 24 304 UNP Q9UN36 NDRG2_HUMAN 24 304
SEQADV 2XMQ ASN A 218 UNP Q9UN36 LEU 218 CONFLICT
SEQADV 2XMQ ASN B 218 UNP Q9UN36 LEU 218 CONFLICT
SEQADV 2XMQ ASN C 218 UNP Q9UN36 LEU 218 CONFLICT
SEQRES 1 A 281 ALA LYS THR HIS SER VAL GLU THR PRO TYR GLY SER VAL
SEQRES 2 A 281 THR PHE THR VAL TYR GLY THR PRO LYS PRO LYS ARG PRO
SEQRES 3 A 281 ALA ILE LEU THR TYR HIS ASP VAL GLY LEU ASN TYR LYS
SEQRES 4 A 281 SER CYS PHE GLN PRO LEU PHE GLN PHE GLU ASP MET GLN
SEQRES 5 A 281 GLU ILE ILE GLN ASN PHE VAL ARG VAL HIS VAL ASP ALA
SEQRES 6 A 281 PRO GLY MET GLU GLU GLY ALA PRO VAL PHE PRO LEU GLY
SEQRES 7 A 281 TYR GLN TYR PRO SER LEU ASP GLN LEU ALA ASP MET ILE
SEQRES 8 A 281 PRO CYS VAL LEU GLN TYR LEU ASN PHE SER THR ILE ILE
SEQRES 9 A 281 GLY VAL GLY VAL GLY ALA GLY ALA TYR ILE LEU ALA ARG
SEQRES 10 A 281 TYR ALA LEU ASN HIS PRO ASP THR VAL GLU GLY LEU VAL
SEQRES 11 A 281 LEU ILE ASN ILE ASP PRO ASN ALA LYS GLY TRP MET ASP
SEQRES 12 A 281 TRP ALA ALA HIS LYS LEU THR GLY LEU THR SER SER ILE
SEQRES 13 A 281 PRO GLU MET ILE LEU GLY HIS LEU PHE SER GLN GLU GLU
SEQRES 14 A 281 LEU SER GLY ASN SER GLU LEU ILE GLN LYS TYR ARG ASN
SEQRES 15 A 281 ILE ILE THR HIS ALA PRO ASN LEU ASP ASN ILE GLU ASN
SEQRES 16 A 281 TYR TRP ASN SER TYR ASN ASN ARG ARG ASP LEU ASN PHE
SEQRES 17 A 281 GLU ARG GLY GLY ASP ILE THR LEU ARG CYS PRO VAL MET
SEQRES 18 A 281 LEU VAL VAL GLY ASP GLN ALA PRO HIS GLU ASP ALA VAL
SEQRES 19 A 281 VAL GLU CYS ASN SER LYS LEU ASP PRO THR GLN THR SER
SEQRES 20 A 281 PHE LEU LYS MET ALA ASP SER GLY GLY GLN PRO GLN LEU
SEQRES 21 A 281 THR GLN PRO GLY LYS LEU THR GLU ALA PHE LYS TYR PHE
SEQRES 22 A 281 LEU GLN GLY MET GLY TYR MET ALA
SEQRES 1 B 281 ALA LYS THR HIS SER VAL GLU THR PRO TYR GLY SER VAL
SEQRES 2 B 281 THR PHE THR VAL TYR GLY THR PRO LYS PRO LYS ARG PRO
SEQRES 3 B 281 ALA ILE LEU THR TYR HIS ASP VAL GLY LEU ASN TYR LYS
SEQRES 4 B 281 SER CYS PHE GLN PRO LEU PHE GLN PHE GLU ASP MET GLN
SEQRES 5 B 281 GLU ILE ILE GLN ASN PHE VAL ARG VAL HIS VAL ASP ALA
SEQRES 6 B 281 PRO GLY MET GLU GLU GLY ALA PRO VAL PHE PRO LEU GLY
SEQRES 7 B 281 TYR GLN TYR PRO SER LEU ASP GLN LEU ALA ASP MET ILE
SEQRES 8 B 281 PRO CYS VAL LEU GLN TYR LEU ASN PHE SER THR ILE ILE
SEQRES 9 B 281 GLY VAL GLY VAL GLY ALA GLY ALA TYR ILE LEU ALA ARG
SEQRES 10 B 281 TYR ALA LEU ASN HIS PRO ASP THR VAL GLU GLY LEU VAL
SEQRES 11 B 281 LEU ILE ASN ILE ASP PRO ASN ALA LYS GLY TRP MET ASP
SEQRES 12 B 281 TRP ALA ALA HIS LYS LEU THR GLY LEU THR SER SER ILE
SEQRES 13 B 281 PRO GLU MET ILE LEU GLY HIS LEU PHE SER GLN GLU GLU
SEQRES 14 B 281 LEU SER GLY ASN SER GLU LEU ILE GLN LYS TYR ARG ASN
SEQRES 15 B 281 ILE ILE THR HIS ALA PRO ASN LEU ASP ASN ILE GLU ASN
SEQRES 16 B 281 TYR TRP ASN SER TYR ASN ASN ARG ARG ASP LEU ASN PHE
SEQRES 17 B 281 GLU ARG GLY GLY ASP ILE THR LEU ARG CYS PRO VAL MET
SEQRES 18 B 281 LEU VAL VAL GLY ASP GLN ALA PRO HIS GLU ASP ALA VAL
SEQRES 19 B 281 VAL GLU CYS ASN SER LYS LEU ASP PRO THR GLN THR SER
SEQRES 20 B 281 PHE LEU LYS MET ALA ASP SER GLY GLY GLN PRO GLN LEU
SEQRES 21 B 281 THR GLN PRO GLY LYS LEU THR GLU ALA PHE LYS TYR PHE
SEQRES 22 B 281 LEU GLN GLY MET GLY TYR MET ALA
SEQRES 1 C 281 ALA LYS THR HIS SER VAL GLU THR PRO TYR GLY SER VAL
SEQRES 2 C 281 THR PHE THR VAL TYR GLY THR PRO LYS PRO LYS ARG PRO
SEQRES 3 C 281 ALA ILE LEU THR TYR HIS ASP VAL GLY LEU ASN TYR LYS
SEQRES 4 C 281 SER CYS PHE GLN PRO LEU PHE GLN PHE GLU ASP MET GLN
SEQRES 5 C 281 GLU ILE ILE GLN ASN PHE VAL ARG VAL HIS VAL ASP ALA
SEQRES 6 C 281 PRO GLY MET GLU GLU GLY ALA PRO VAL PHE PRO LEU GLY
SEQRES 7 C 281 TYR GLN TYR PRO SER LEU ASP GLN LEU ALA ASP MET ILE
SEQRES 8 C 281 PRO CYS VAL LEU GLN TYR LEU ASN PHE SER THR ILE ILE
SEQRES 9 C 281 GLY VAL GLY VAL GLY ALA GLY ALA TYR ILE LEU ALA ARG
SEQRES 10 C 281 TYR ALA LEU ASN HIS PRO ASP THR VAL GLU GLY LEU VAL
SEQRES 11 C 281 LEU ILE ASN ILE ASP PRO ASN ALA LYS GLY TRP MET ASP
SEQRES 12 C 281 TRP ALA ALA HIS LYS LEU THR GLY LEU THR SER SER ILE
SEQRES 13 C 281 PRO GLU MET ILE LEU GLY HIS LEU PHE SER GLN GLU GLU
SEQRES 14 C 281 LEU SER GLY ASN SER GLU LEU ILE GLN LYS TYR ARG ASN
SEQRES 15 C 281 ILE ILE THR HIS ALA PRO ASN LEU ASP ASN ILE GLU ASN
SEQRES 16 C 281 TYR TRP ASN SER TYR ASN ASN ARG ARG ASP LEU ASN PHE
SEQRES 17 C 281 GLU ARG GLY GLY ASP ILE THR LEU ARG CYS PRO VAL MET
SEQRES 18 C 281 LEU VAL VAL GLY ASP GLN ALA PRO HIS GLU ASP ALA VAL
SEQRES 19 C 281 VAL GLU CYS ASN SER LYS LEU ASP PRO THR GLN THR SER
SEQRES 20 C 281 PHE LEU LYS MET ALA ASP SER GLY GLY GLN PRO GLN LEU
SEQRES 21 C 281 THR GLN PRO GLY LYS LEU THR GLU ALA PHE LYS TYR PHE
SEQRES 22 C 281 LEU GLN GLY MET GLY TYR MET ALA
HET ACT A1305 4
HET ACT B1305 4
HET ACT C1305 4
HETNAM ACT ACETATE ION
FORMUL 4 ACT 3(C2 H3 O2 1-)
FORMUL 5 HOH *93(H2 O)
HELIX 1 1 ASN A 60 PHE A 65 1 6
HELIX 2 2 PHE A 65 PHE A 71 1 7
HELIX 3 3 PHE A 71 GLN A 79 1 9
HELIX 4 4 SER A 106 ASP A 112 1 7
HELIX 5 5 MET A 113 ASN A 122 1 10
HELIX 6 6 GLY A 132 HIS A 145 1 14
HELIX 7 7 GLY A 163 LEU A 175 1 13
HELIX 8 8 SER A 178 PHE A 188 1 11
HELIX 9 9 SER A 189 ASN A 196 1 8
HELIX 10 10 SER A 197 HIS A 209 1 13
HELIX 11 11 ASN A 212 ASN A 225 1 14
HELIX 12 12 HIS A 253 LEU A 264 1 12
HELIX 13 13 GLN A 280 GLN A 285 1 6
HELIX 14 14 GLN A 285 MET A 300 1 16
HELIX 15 15 ASN B 60 PHE B 65 1 6
HELIX 16 16 PHE B 65 PHE B 71 1 7
HELIX 17 17 PHE B 71 GLN B 79 1 9
HELIX 18 18 SER B 106 ASN B 122 1 17
HELIX 19 19 GLY B 132 HIS B 145 1 14
HELIX 20 20 GLY B 163 LEU B 175 1 13
HELIX 21 21 SER B 178 PHE B 188 1 11
HELIX 22 22 SER B 189 ASN B 196 1 8
HELIX 23 23 SER B 197 HIS B 209 1 13
HELIX 24 24 ASN B 212 ASN B 225 1 14
HELIX 25 25 HIS B 253 LEU B 264 1 12
HELIX 26 26 ASP B 265 THR B 267 5 3
HELIX 27 27 GLN B 280 GLN B 285 1 6
HELIX 28 28 GLN B 285 MET B 300 1 16
HELIX 29 29 ASN C 60 PHE C 65 1 6
HELIX 30 30 PHE C 65 PHE C 71 1 7
HELIX 31 31 PHE C 71 GLN C 79 1 9
HELIX 32 32 SER C 106 MET C 113 1 8
HELIX 33 33 MET C 113 ASN C 122 1 10
HELIX 34 34 GLY C 132 HIS C 145 1 14
HELIX 35 35 GLY C 163 GLY C 174 1 12
HELIX 36 36 SER C 178 PHE C 188 1 11
HELIX 37 37 SER C 189 ASN C 196 1 8
HELIX 38 38 SER C 197 HIS C 209 1 13
HELIX 39 39 ASN C 212 ARG C 226 1 15
HELIX 40 40 HIS C 253 SER C 262 1 10
HELIX 41 41 ASP C 265 THR C 267 5 3
HELIX 42 42 GLN C 280 GLN C 285 1 6
HELIX 43 43 GLN C 285 MET C 300 1 16
SHEET 1 AA 8 LYS A 25 THR A 31 0
SHEET 2 AA 8 GLY A 34 TYR A 41 -1 O GLY A 34 N THR A 31
SHEET 3 AA 8 ARG A 83 ASP A 87 -1 O ARG A 83 N TYR A 41
SHEET 4 AA 8 ALA A 50 TYR A 54 1 O ILE A 51 N VAL A 84
SHEET 5 AA 8 ILE A 126 VAL A 131 1 O ILE A 127 N LEU A 52
SHEET 6 AA 8 VAL A 149 ILE A 155 1 N GLU A 150 O ILE A 126
SHEET 7 AA 8 VAL A 243 GLY A 248 1 O MET A 244 N LEU A 154
SHEET 8 AA 8 THR A 269 MET A 274 1 O SER A 270 N LEU A 245
SHEET 1 BA 8 LYS B 25 THR B 31 0
SHEET 2 BA 8 GLY B 34 TYR B 41 -1 O GLY B 34 N THR B 31
SHEET 3 BA 8 VAL B 82 ASP B 87 -1 O ARG B 83 N TYR B 41
SHEET 4 BA 8 ALA B 50 TYR B 54 1 O ILE B 51 N VAL B 84
SHEET 5 BA 8 ILE B 126 VAL B 131 1 O ILE B 127 N LEU B 52
SHEET 6 BA 8 VAL B 149 ILE B 155 1 N GLU B 150 O ILE B 126
SHEET 7 BA 8 VAL B 243 GLY B 248 1 O MET B 244 N LEU B 154
SHEET 8 BA 8 THR B 269 MET B 274 1 O SER B 270 N LEU B 245
SHEET 1 CA 8 LYS C 25 THR C 31 0
SHEET 2 CA 8 GLY C 34 TYR C 41 -1 O GLY C 34 N THR C 31
SHEET 3 CA 8 ARG C 83 ASP C 87 -1 O ARG C 83 N TYR C 41
SHEET 4 CA 8 ALA C 50 TYR C 54 1 O ILE C 51 N VAL C 84
SHEET 5 CA 8 ILE C 126 VAL C 131 1 O ILE C 127 N LEU C 52
SHEET 6 CA 8 VAL C 149 ILE C 155 1 N GLU C 150 O ILE C 126
SHEET 7 CA 8 VAL C 243 GLY C 248 1 O MET C 244 N LEU C 154
SHEET 8 CA 8 THR C 269 MET C 274 1 O SER C 270 N LEU C 245
SITE 1 AC1 7 TYR B 41 TYR B 61 PHE B 69 GLN B 75
SITE 2 AC1 7 ARG B 83 HIS B 85 HOH B2023
SITE 1 AC2 6 TYR A 41 TYR A 61 PHE A 69 GLN A 75
SITE 2 AC2 6 ARG A 83 HIS A 85
SITE 1 AC3 6 TYR C 41 TYR C 61 PHE C 69 GLN C 75
SITE 2 AC3 6 ARG C 83 HIS C 85
CRYST1 86.411 88.897 126.799 90.00 90.00 90.00 P 21 21 21 12
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.011573 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011249 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007886 0.00000
TER 2206 ALA A 304
TER 4412 ALA B 304
TER 6618 ALA C 304
MASTER 451 0 3 43 24 0 6 6 6720 3 12 66
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