| content |
HEADER LYASE 18-APR-11 3RKS
TITLE CRYSTAL STRUCTURE OF THE MANIHOT ESCULENTA HYDROXYNITRILE LYASE
TITLE 2 (MEHNL) K176P MUTANT
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: HYDROXYNITRILASE;
COMPND 3 CHAIN: A, B, C, D;
COMPND 4 SYNONYM: (S)-ACETONE-CYANOHYDRIN LYASE, (S)-HYDROXYNITRILE LYASE,
COMPND 5 OXYNITRILASE;
COMPND 6 EC: 4.1.2.37;
COMPND 7 ENGINEERED: YES;
COMPND 8 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: MANIHOT ESCULENTA;
SOURCE 3 ORGANISM_COMMON: MANIOC,TAPIOCA,YUCA;
SOURCE 4 ORGANISM_TAXID: 3983;
SOURCE 5 GENE: HNL;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS REVERSIBLE, STEREOSPECIFIC METABOLISM, CYANOHYDRINS, NATURAL LIGAND,
KEYWDS 2 ACETONE, ACETATE, ACETATE CYANOHYDRIN, LYASE
EXPDTA X-RAY DIFFRACTION
AUTHOR C.B.C.CIELO,T.YAMANE,Y.ASANO,M.DADASHIPOUR,A.SUZUKI,T.MIZUSHIMA,
AUTHOR 2 H.KOMEDA
REVDAT 1 20-JUN-12 3RKS 0
JRNL AUTH C.B.C.CIELO,T.YAMANE,Y.ASANO,M.DADASHIPOUR,A.SUZUKI,
JRNL AUTH 2 T.MIZUSHIMA,H.KOMEDA
JRNL TITL CRYSTALLOGRAPHIC STUDIES OF MANIHOT ESCULENTA HYDROXYNITRILE
JRNL TITL 2 LYASE LYSINE-TO-PROLINE MUTANTS
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 2.50 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0109
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) : 2.50
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.19
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5
REMARK 3 NUMBER OF REFLECTIONS : 36063
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) : 0.177
REMARK 3 R VALUE (WORKING SET) : 0.174
REMARK 3 FREE R VALUE : 0.238
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1895
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) : 2.50
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2444
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.27
REMARK 3 BIN R VALUE (WORKING SET) : 0.2390
REMARK 3 BIN FREE R VALUE SET COUNT : 124
REMARK 3 BIN FREE R VALUE : 0.3530
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 8288
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 12
REMARK 3 SOLVENT ATOMS : 507
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.78
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.01000
REMARK 3 B22 (A**2) : 0.01000
REMARK 3 B33 (A**2) : 0.00000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.301
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.000
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.002
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL
REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
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): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
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): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
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 : NULL
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 : 1.40
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 3RKS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-APR-11.
REMARK 100 THE RCSB ID CODE IS RCSB065054.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 28-APR-09
REMARK 200 TEMPERATURE (KELVIN) : NULL
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E DW
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.54
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS VII
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36063
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500
REMARK 200 RESOLUTION RANGE LOW (A) : 100.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 46.88
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 2% PEG 400, 2.0M AMMONIUM SULPHATE,
REMARK 280 0.1M HEPES-NA (PH 7.5), 10% GLYCEROL, VAPOR DIFFUSION, HANGING
REMARK 280 DROP, TEMPERATURE 293K
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 43.31400
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 68.72050
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.70700
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 68.72050
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.31400
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.70700
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
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1740 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 19420 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1760 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 19500 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D
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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 OE2 GLU B 72 O HOH B 525 1.41
REMARK 500 O HOH C 496 O HOH C 512 1.81
REMARK 500 O HOH C 332 O HOH C 535 1.90
REMARK 500 OD1 ASP A 95 O HOH A 479 1.93
REMARK 500 O HOH A 487 O HOH C 335 2.05
REMARK 500 O HOH D 480 O HOH D 497 2.11
REMARK 500 O HOH A 377 O HOH A 381 2.16
REMARK 500 O HOH C 323 O HOH C 384 2.17
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 O HOH A 409 O HOH B 322 2554 2.15
REMARK 500
REMARK 500 REMARK: NULL
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 245 CG GLU A 245 CD 0.095
REMARK 500 GLU A 245 CD GLU A 245 OE2 0.067
REMARK 500 GLU B 245 CG GLU B 245 CD 0.102
REMARK 500 GLU B 245 CD GLU B 245 OE2 0.071
REMARK 500 GLU C 245 CG GLU C 245 CD 0.090
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 ARG B 129 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 ARG B 129 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES
REMARK 500 ARG C 155 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES
REMARK 500 ARG D 28 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 ASP D 37 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES
REMARK 500 ASP D 255 CB - CG - OD1 ANGL. DEV. = 5.4 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 CYS A 13 -31.97 79.93
REMARK 500 HIS A 14 -160.13 -79.87
REMARK 500 SER A 80 -111.59 47.11
REMARK 500 TYR A 93 37.98 -145.36
REMARK 500 ARG A 129 -116.41 69.57
REMARK 500 ILE A 210 -51.07 -121.28
REMARK 500 CYS B 13 -30.24 78.78
REMARK 500 SER B 80 -112.31 47.70
REMARK 500 ASN B 104 53.82 39.04
REMARK 500 ARG B 129 -119.33 65.73
REMARK 500 THR B 160 -58.84 -27.08
REMARK 500 LYS B 242 37.96 -147.10
REMARK 500 CYS C 13 -31.64 79.74
REMARK 500 HIS C 14 -158.88 -80.65
REMARK 500 SER C 80 -115.49 30.23
REMARK 500 VAL C 94 -36.92 -37.24
REMARK 500 ARG C 129 -126.24 69.70
REMARK 500 ILE C 210 -47.25 -133.69
REMARK 500 ILE D 12 150.70 -49.98
REMARK 500 CYS D 13 -20.21 71.42
REMARK 500 HIS D 14 -155.03 -93.52
REMARK 500 GLN D 70 132.27 -36.06
REMARK 500 SER D 80 -111.01 34.59
REMARK 500 TYR D 93 38.68 -147.46
REMARK 500 ARG D 129 -124.38 66.86
REMARK 500 PHE D 159 45.62 -106.28
REMARK 500 ILE D 210 -50.53 -128.11
REMARK 500 TYR D 223 87.62 -171.06
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 TYR B 257 ALA B 258 148.65
REMARK 500 TYR C 257 ALA C 258 141.97
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 GOL C 259
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL D 259
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3RKT RELATED DB: PDB
DBREF 3RKS A 1 258 UNP P52705 HNL_MANES 1 258
DBREF 3RKS B 1 258 UNP P52705 HNL_MANES 1 258
DBREF 3RKS C 1 258 UNP P52705 HNL_MANES 1 258
DBREF 3RKS D 1 258 UNP P52705 HNL_MANES 1 258
SEQADV 3RKS PRO A 176 UNP P52705 LYS 176 ENGINEERED MUTATION
SEQADV 3RKS PRO B 176 UNP P52705 LYS 176 ENGINEERED MUTATION
SEQADV 3RKS PRO C 176 UNP P52705 LYS 176 ENGINEERED MUTATION
SEQADV 3RKS PRO D 176 UNP P52705 LYS 176 ENGINEERED MUTATION
SEQRES 1 A 258 MET VAL THR ALA HIS PHE VAL LEU ILE HIS THR ILE CYS
SEQRES 2 A 258 HIS GLY ALA TRP ILE TRP HIS LYS LEU LYS PRO ALA LEU
SEQRES 3 A 258 GLU ARG ALA GLY HIS LYS VAL THR ALA LEU ASP MET ALA
SEQRES 4 A 258 ALA SER GLY ILE ASP PRO ARG GLN ILE GLU GLN ILE ASN
SEQRES 5 A 258 SER PHE ASP GLU TYR SER GLU PRO LEU LEU THR PHE LEU
SEQRES 6 A 258 GLU LYS LEU PRO GLN GLY GLU LYS VAL ILE ILE VAL GLY
SEQRES 7 A 258 GLU SER CYS ALA GLY LEU ASN ILE ALA ILE ALA ALA ASP
SEQRES 8 A 258 ARG TYR VAL ASP LYS ILE ALA ALA GLY VAL PHE HIS ASN
SEQRES 9 A 258 SER LEU LEU PRO ASP THR VAL HIS SER PRO SER TYR THR
SEQRES 10 A 258 VAL GLU LYS LEU LEU GLU SER PHE PRO ASP TRP ARG ASP
SEQRES 11 A 258 THR GLU TYR PHE THR PHE THR ASN ILE THR GLY GLU THR
SEQRES 12 A 258 ILE THR THR MET LYS LEU GLY PHE VAL LEU LEU ARG GLU
SEQRES 13 A 258 ASN LEU PHE THR LYS CYS THR ASP GLY GLU TYR GLU LEU
SEQRES 14 A 258 ALA LYS MET VAL MET ARG PRO GLY SER LEU PHE GLN ASN
SEQRES 15 A 258 VAL LEU ALA GLN ARG PRO LYS PHE THR GLU LYS GLY TYR
SEQRES 16 A 258 GLY SER ILE LYS LYS VAL TYR ILE TRP THR ASP GLN ASP
SEQRES 17 A 258 LYS ILE PHE LEU PRO ASP PHE GLN ARG TRP GLN ILE ALA
SEQRES 18 A 258 ASN TYR LYS PRO ASP LYS VAL TYR GLN VAL GLN GLY GLY
SEQRES 19 A 258 ASP HIS LYS LEU GLN LEU THR LYS THR GLU GLU VAL ALA
SEQRES 20 A 258 HIS ILE LEU GLN GLU VAL ALA ASP ALA TYR ALA
SEQRES 1 B 258 MET VAL THR ALA HIS PHE VAL LEU ILE HIS THR ILE CYS
SEQRES 2 B 258 HIS GLY ALA TRP ILE TRP HIS LYS LEU LYS PRO ALA LEU
SEQRES 3 B 258 GLU ARG ALA GLY HIS LYS VAL THR ALA LEU ASP MET ALA
SEQRES 4 B 258 ALA SER GLY ILE ASP PRO ARG GLN ILE GLU GLN ILE ASN
SEQRES 5 B 258 SER PHE ASP GLU TYR SER GLU PRO LEU LEU THR PHE LEU
SEQRES 6 B 258 GLU LYS LEU PRO GLN GLY GLU LYS VAL ILE ILE VAL GLY
SEQRES 7 B 258 GLU SER CYS ALA GLY LEU ASN ILE ALA ILE ALA ALA ASP
SEQRES 8 B 258 ARG TYR VAL ASP LYS ILE ALA ALA GLY VAL PHE HIS ASN
SEQRES 9 B 258 SER LEU LEU PRO ASP THR VAL HIS SER PRO SER TYR THR
SEQRES 10 B 258 VAL GLU LYS LEU LEU GLU SER PHE PRO ASP TRP ARG ASP
SEQRES 11 B 258 THR GLU TYR PHE THR PHE THR ASN ILE THR GLY GLU THR
SEQRES 12 B 258 ILE THR THR MET LYS LEU GLY PHE VAL LEU LEU ARG GLU
SEQRES 13 B 258 ASN LEU PHE THR LYS CYS THR ASP GLY GLU TYR GLU LEU
SEQRES 14 B 258 ALA LYS MET VAL MET ARG PRO GLY SER LEU PHE GLN ASN
SEQRES 15 B 258 VAL LEU ALA GLN ARG PRO LYS PHE THR GLU LYS GLY TYR
SEQRES 16 B 258 GLY SER ILE LYS LYS VAL TYR ILE TRP THR ASP GLN ASP
SEQRES 17 B 258 LYS ILE PHE LEU PRO ASP PHE GLN ARG TRP GLN ILE ALA
SEQRES 18 B 258 ASN TYR LYS PRO ASP LYS VAL TYR GLN VAL GLN GLY GLY
SEQRES 19 B 258 ASP HIS LYS LEU GLN LEU THR LYS THR GLU GLU VAL ALA
SEQRES 20 B 258 HIS ILE LEU GLN GLU VAL ALA ASP ALA TYR ALA
SEQRES 1 C 258 MET VAL THR ALA HIS PHE VAL LEU ILE HIS THR ILE CYS
SEQRES 2 C 258 HIS GLY ALA TRP ILE TRP HIS LYS LEU LYS PRO ALA LEU
SEQRES 3 C 258 GLU ARG ALA GLY HIS LYS VAL THR ALA LEU ASP MET ALA
SEQRES 4 C 258 ALA SER GLY ILE ASP PRO ARG GLN ILE GLU GLN ILE ASN
SEQRES 5 C 258 SER PHE ASP GLU TYR SER GLU PRO LEU LEU THR PHE LEU
SEQRES 6 C 258 GLU LYS LEU PRO GLN GLY GLU LYS VAL ILE ILE VAL GLY
SEQRES 7 C 258 GLU SER CYS ALA GLY LEU ASN ILE ALA ILE ALA ALA ASP
SEQRES 8 C 258 ARG TYR VAL ASP LYS ILE ALA ALA GLY VAL PHE HIS ASN
SEQRES 9 C 258 SER LEU LEU PRO ASP THR VAL HIS SER PRO SER TYR THR
SEQRES 10 C 258 VAL GLU LYS LEU LEU GLU SER PHE PRO ASP TRP ARG ASP
SEQRES 11 C 258 THR GLU TYR PHE THR PHE THR ASN ILE THR GLY GLU THR
SEQRES 12 C 258 ILE THR THR MET LYS LEU GLY PHE VAL LEU LEU ARG GLU
SEQRES 13 C 258 ASN LEU PHE THR LYS CYS THR ASP GLY GLU TYR GLU LEU
SEQRES 14 C 258 ALA LYS MET VAL MET ARG PRO GLY SER LEU PHE GLN ASN
SEQRES 15 C 258 VAL LEU ALA GLN ARG PRO LYS PHE THR GLU LYS GLY TYR
SEQRES 16 C 258 GLY SER ILE LYS LYS VAL TYR ILE TRP THR ASP GLN ASP
SEQRES 17 C 258 LYS ILE PHE LEU PRO ASP PHE GLN ARG TRP GLN ILE ALA
SEQRES 18 C 258 ASN TYR LYS PRO ASP LYS VAL TYR GLN VAL GLN GLY GLY
SEQRES 19 C 258 ASP HIS LYS LEU GLN LEU THR LYS THR GLU GLU VAL ALA
SEQRES 20 C 258 HIS ILE LEU GLN GLU VAL ALA ASP ALA TYR ALA
SEQRES 1 D 258 MET VAL THR ALA HIS PHE VAL LEU ILE HIS THR ILE CYS
SEQRES 2 D 258 HIS GLY ALA TRP ILE TRP HIS LYS LEU LYS PRO ALA LEU
SEQRES 3 D 258 GLU ARG ALA GLY HIS LYS VAL THR ALA LEU ASP MET ALA
SEQRES 4 D 258 ALA SER GLY ILE ASP PRO ARG GLN ILE GLU GLN ILE ASN
SEQRES 5 D 258 SER PHE ASP GLU TYR SER GLU PRO LEU LEU THR PHE LEU
SEQRES 6 D 258 GLU LYS LEU PRO GLN GLY GLU LYS VAL ILE ILE VAL GLY
SEQRES 7 D 258 GLU SER CYS ALA GLY LEU ASN ILE ALA ILE ALA ALA ASP
SEQRES 8 D 258 ARG TYR VAL ASP LYS ILE ALA ALA GLY VAL PHE HIS ASN
SEQRES 9 D 258 SER LEU LEU PRO ASP THR VAL HIS SER PRO SER TYR THR
SEQRES 10 D 258 VAL GLU LYS LEU LEU GLU SER PHE PRO ASP TRP ARG ASP
SEQRES 11 D 258 THR GLU TYR PHE THR PHE THR ASN ILE THR GLY GLU THR
SEQRES 12 D 258 ILE THR THR MET LYS LEU GLY PHE VAL LEU LEU ARG GLU
SEQRES 13 D 258 ASN LEU PHE THR LYS CYS THR ASP GLY GLU TYR GLU LEU
SEQRES 14 D 258 ALA LYS MET VAL MET ARG PRO GLY SER LEU PHE GLN ASN
SEQRES 15 D 258 VAL LEU ALA GLN ARG PRO LYS PHE THR GLU LYS GLY TYR
SEQRES 16 D 258 GLY SER ILE LYS LYS VAL TYR ILE TRP THR ASP GLN ASP
SEQRES 17 D 258 LYS ILE PHE LEU PRO ASP PHE GLN ARG TRP GLN ILE ALA
SEQRES 18 D 258 ASN TYR LYS PRO ASP LYS VAL TYR GLN VAL GLN GLY GLY
SEQRES 19 D 258 ASP HIS LYS LEU GLN LEU THR LYS THR GLU GLU VAL ALA
SEQRES 20 D 258 HIS ILE LEU GLN GLU VAL ALA ASP ALA TYR ALA
HET GOL C 259 6
HET GOL D 259 6
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 5 GOL 2(C3 H8 O3)
FORMUL 7 HOH *507(H2 O)
HELIX 1 1 GLY A 15 HIS A 20 5 6
HELIX 2 2 LYS A 21 ALA A 29 1 9
HELIX 3 3 GLN A 47 ILE A 51 5 5
HELIX 4 4 SER A 53 SER A 58 1 6
HELIX 5 5 SER A 58 LYS A 67 1 10
HELIX 6 6 ALA A 82 VAL A 94 1 13
HELIX 7 7 SER A 115 PHE A 125 1 11
HELIX 8 8 GLY A 150 ASN A 157 1 8
HELIX 9 9 THR A 163 MET A 174 1 12
HELIX 10 10 PHE A 180 ALA A 185 1 6
HELIX 11 11 GLY A 194 ILE A 198 5 5
HELIX 12 12 LEU A 212 TYR A 223 1 12
HELIX 13 13 LYS A 237 LYS A 242 1 6
HELIX 14 14 LYS A 242 ALA A 258 1 17
HELIX 15 15 GLY B 15 HIS B 20 5 6
HELIX 16 16 LYS B 21 ALA B 29 1 9
HELIX 17 17 GLN B 47 ILE B 51 5 5
HELIX 18 18 SER B 53 SER B 58 1 6
HELIX 19 19 SER B 58 LEU B 68 1 11
HELIX 20 20 ALA B 82 VAL B 94 1 13
HELIX 21 21 SER B 115 PHE B 125 1 11
HELIX 22 22 GLY B 150 ASN B 157 1 8
HELIX 23 23 THR B 163 MET B 174 1 12
HELIX 24 24 PHE B 180 ALA B 185 1 6
HELIX 25 25 GLY B 194 ILE B 198 5 5
HELIX 26 26 LEU B 212 TYR B 223 1 12
HELIX 27 27 LYS B 237 LYS B 242 1 6
HELIX 28 28 LYS B 242 ALA B 258 1 17
HELIX 29 29 GLY C 15 HIS C 20 5 6
HELIX 30 30 LYS C 21 ALA C 29 1 9
HELIX 31 31 GLN C 47 ILE C 51 5 5
HELIX 32 32 SER C 53 SER C 58 1 6
HELIX 33 33 SER C 58 LEU C 68 1 11
HELIX 34 34 ALA C 82 VAL C 94 1 13
HELIX 35 35 SER C 115 PHE C 125 1 11
HELIX 36 36 GLY C 150 ASN C 157 1 8
HELIX 37 37 THR C 163 MET C 174 1 12
HELIX 38 38 PHE C 180 GLN C 186 1 7
HELIX 39 39 GLY C 194 ILE C 198 5 5
HELIX 40 40 LEU C 212 TYR C 223 1 12
HELIX 41 41 LYS C 237 LYS C 242 1 6
HELIX 42 42 LYS C 242 ALA C 258 1 17
HELIX 43 43 GLY D 15 HIS D 20 5 6
HELIX 44 44 LYS D 21 ALA D 29 1 9
HELIX 45 45 GLN D 47 ILE D 51 5 5
HELIX 46 46 SER D 53 SER D 58 1 6
HELIX 47 47 SER D 58 LEU D 68 1 11
HELIX 48 48 ALA D 82 VAL D 94 1 13
HELIX 49 49 SER D 115 PHE D 125 1 11
HELIX 50 50 GLY D 150 ASN D 157 1 8
HELIX 51 51 THR D 163 MET D 174 1 12
HELIX 52 52 PHE D 180 GLN D 186 1 7
HELIX 53 53 GLY D 194 ILE D 198 5 5
HELIX 54 54 LEU D 212 TYR D 223 1 12
HELIX 55 55 LYS D 237 LYS D 242 1 6
HELIX 56 56 LYS D 242 ALA D 258 1 17
SHEET 1 A 6 LYS A 32 LEU A 36 0
SHEET 2 A 6 HIS A 5 ILE A 9 1 N LEU A 8 O THR A 34
SHEET 3 A 6 VAL A 74 SER A 80 1 O VAL A 77 N ILE A 9
SHEET 4 A 6 ILE A 97 SER A 105 1 O VAL A 101 N ILE A 76
SHEET 5 A 6 LYS A 200 TRP A 204 1 O ILE A 203 N PHE A 102
SHEET 6 A 6 LYS A 227 GLN A 230 1 O TYR A 229 N TYR A 202
SHEET 1 B 2 GLU A 132 THR A 137 0
SHEET 2 B 2 THR A 143 LYS A 148 -1 O THR A 146 N PHE A 134
SHEET 1 C 6 LYS B 32 LEU B 36 0
SHEET 2 C 6 HIS B 5 ILE B 9 1 N PHE B 6 O THR B 34
SHEET 3 C 6 VAL B 74 GLU B 79 1 O VAL B 77 N VAL B 7
SHEET 4 C 6 ILE B 97 HIS B 103 1 O VAL B 101 N ILE B 76
SHEET 5 C 6 LYS B 200 TRP B 204 1 O ILE B 203 N PHE B 102
SHEET 6 C 6 LYS B 227 GLN B 230 1 O LYS B 227 N TYR B 202
SHEET 1 D 2 GLU B 132 THR B 137 0
SHEET 2 D 2 THR B 143 LYS B 148 -1 O ILE B 144 N PHE B 136
SHEET 1 E 6 LYS C 32 LEU C 36 0
SHEET 2 E 6 HIS C 5 ILE C 9 1 N LEU C 8 O THR C 34
SHEET 3 E 6 VAL C 74 SER C 80 1 O ILE C 75 N VAL C 7
SHEET 4 E 6 ILE C 97 SER C 105 1 O ALA C 98 N VAL C 74
SHEET 5 E 6 LYS C 200 TRP C 204 1 O ILE C 203 N PHE C 102
SHEET 6 E 6 LYS C 227 GLN C 230 1 O TYR C 229 N TYR C 202
SHEET 1 F 2 GLU C 132 THR C 137 0
SHEET 2 F 2 THR C 143 LYS C 148 -1 O ILE C 144 N PHE C 136
SHEET 1 G 6 LYS D 32 LEU D 36 0
SHEET 2 G 6 HIS D 5 ILE D 9 1 N LEU D 8 O THR D 34
SHEET 3 G 6 VAL D 74 SER D 80 1 O VAL D 77 N ILE D 9
SHEET 4 G 6 ILE D 97 SER D 105 1 O ALA D 98 N VAL D 74
SHEET 5 G 6 LYS D 199 TRP D 204 1 O ILE D 203 N PHE D 102
SHEET 6 G 6 LYS D 227 GLN D 230 1 O LYS D 227 N TYR D 202
SHEET 1 H 3 GLU D 132 THR D 137 0
SHEET 2 H 3 THR D 143 LYS D 148 -1 O ILE D 144 N PHE D 136
SHEET 3 H 3 GLY D 177 SER D 178 -1 O GLY D 177 N MET D 147
SITE 1 AC1 10 ILE A 43 ASP A 44 PRO A 45 GLN A 47
SITE 2 AC1 10 ARG A 175 ILE C 43 ASP C 44 PRO C 45
SITE 3 AC1 10 GLN C 47 ARG C 175
SITE 1 AC2 10 ILE B 43 ASP B 44 PRO B 45 GLN B 47
SITE 2 AC2 10 ARG B 175 ILE D 43 ASP D 44 PRO D 45
SITE 3 AC2 10 GLN D 47 ARG D 175
CRYST1 86.628 91.414 137.441 90.00 90.00 90.00 P 21 21 21 16
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 0.011544 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010939 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007276 0.00000
TER 2073 ALA A 258
TER 4146 ALA B 258
TER 6219 ALA C 258
TER 8292 ALA D 258
MASTER 399 0 2 56 33 0 6 6 8807 4 12 80
END |