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HEADER HYDROLASE 07-DEC-98 2DFP
TITLE X-RAY STRUCTURE OF AGED DI-ISOPROPYL-PHOSPHORO-FLUORIDATE
TITLE 2 (DFP) BOUND TO ACETYLCHOLINESTERASE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ACETYLCHOLINESTERASE;
COMPND 3 CHAIN: A;
COMPND 4 EC: 3.1.1.7;
COMPND 5 BIOLOGICAL_UNIT: DIMER;
COMPND 6 OTHER_DETAILS: THE PROTEIN, ACETYLCHOLINESTERASE, WAS
COMPND 7 TREATED WITH THE ORGANOPHOSPHATE, DFP, PRIOR TO
COMPND 8 CRYSTALLIZATION.
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: TORPEDO CALIFORNICA;
SOURCE 3 ORGANISM_COMMON: PACIFIC ELECTRIC RAY;
SOURCE 4 VARIANT: G2 FORM;
SOURCE 5 ORGAN: ELECTRIC ORGAN;
SOURCE 6 TISSUE: ELECTROPLAQUE
KEYWDS AGED ORGANOPHOSPHATE, DFP, SERINE HYDROLASE, SERINE
KEYWDS 2 HYDROLASE, NEUROTRANSMITTER CLEAVAGE, CATALYTIC TRIAD,
KEYWDS 3 ALPHA/BETA HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR G.KRYGER,C.B.MILLARD,I.SILMAN,J.L.SUSSMAN
REVDAT 1 28-JUN-99 2DFP 0
JRNL AUTH C.B.MILLARD,G.KRYGER,A.ORDENTLICHT,H.M.GREENBLATT,
JRNL AUTH 2 M.HAREL,M.L.RAVES,Y.SEGALL,D.BARAK,A.SHAFFERMAN,
JRNL AUTH 3 I.SILMAN,J.L.SUSSMAN
JRNL TITL CRYSTAL STRUCTURES OF AGED PHOSPHYLATED
JRNL TITL 2 ACETYLCHOLINESTERASE: NERVE AGENT REACTION
JRNL TITL 3 PRODUCTS AT THE ATOMIC LEVEL
JRNL REF BIOCHEMISTRY V. 38 7032 1999
JRNL REFN ASTM BICHAW US ISSN 0006-2960 0033
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH J.L.SUSSMAN,M.HAREL,F.FROLOW,C.OEFNER,A.GOLDMAN,
REMARK 1 AUTH 2 L.TOKER,I.SILMAN
REMARK 1 TITL ATOMIC STRUCTURE OF ACETYLCHOLINESTERASE FROM
REMARK 1 TITL 2 TORPEDO CALIFORNICA: A PROTOTYPIC
REMARK 1 TITL 3 ACETYLCHOLINE-BINDING PROTEIN
REMARK 1 REF SCIENCE V. 253 872 1991
REMARK 1 REFN ASTM SCIEAS US ISSN 0036-8075 0038
REMARK 2
REMARK 2 RESOLUTION. 2.30 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 0.4
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,
REMARK 3 : READ,RICE,SIMONSON,WARREN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.0
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 OUTLIER CUTOFF HIGH (RMS(ABS(F))) : 2409412.92000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.7
REMARK 3 NUMBER OF REFLECTIONS : 42208
REMARK 3
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 SET) : 0.186
REMARK 3 FREE R VALUE : 0.228
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.400
REMARK 3 FREE R VALUE TEST SET COUNT : 1874
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 10
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.38
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 65.20
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2760
REMARK 3 BIN R VALUE (WORKING SET) : 0.3530
REMARK 3 BIN FREE R VALUE : 0.3630
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 129
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.03
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4270
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 82
REMARK 3 SOLVENT ATOMS : 376
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 45.70
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.40
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 8.06000
REMARK 3 B22 (A**2) : 8.06000
REMARK 3 B33 (A**2) : -16.10000
REMARK 3 B12 (A**2) : 8.63000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.28
REMARK 3 ESD FROM SIGMAA (A) : 0.450
REMARK 3 LOW RESOLUTION CUTOFF (A) : 4.00
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.35
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.49
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.019
REMARK 3 BOND ANGLES (DEGREES) : 1.90
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.50
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.31
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : OVERALL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.34
REMARK 3 BSOL : 44.45
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM
REMARK 3 PARAMETER FILE 2 : CARBOHYDRATE.PARAM
REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM
REMARK 3 PARAMETER FILE 4 : DFP.PAR, MES.PAR
REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
REMARK 3 TOPOLOGY FILE 2 : CARBOHYDRATE.TOP
REMARK 3 TOPOLOGY FILE 3 : WATER.TOP
REMARK 3 TOPOLOGY FILE 4 : DFP.TOP, MES.TOP
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED
REMARK 4
REMARK 4 2DFP COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998
REMARK 7
REMARK 7 TORPEDO CALIFONICA ACETYLCHOLINESTERASE IS A G2 DIMER IN
REMARK 7 SOLUTION (SEE SUSSMAN 1988). THE ASYMMETRIC UNIT CONTAINS A
REMARK 7 MONOMER, WITH THE CRYSTALLOGRAPHIC TWO-FOLD AXIS RELATING
REMARK 7 THE TWO MONOMERS IN A DIMER. BIOMOLECULE: THE ENZYME IS A
REMARK 7 GPI-ANCHORED DIMER, THE TWO MONOMERS IN THE DIMER ARE
REMARK 7 RELATED BY THE CRYSTALLOGRAPHIC TWO-FOLD SYMMETRY AND THUS
REMARK 7 GENERATE A FOUR HELIX BUNDLE A365-A375 AND A518-A535.
REMARK 7 DFP WAS REACTED WITH THE ENZYME IN SOLUTION.
REMARK 7 THE SOLUTION OF THE INHIBITED ENZYME WAS DIALYZED TO REMOVE
REMARK 7 EXCESS ORGANOPHOSPHATE, CHECKED FOR ACTIVITY AND FOUND TO
REMARK 7 REACT LIKE "AGED" PHOSPHYLATED ACHE, AND THEN SUBJECTED TO
REMARK 7 CRYSTALLIZATION. THIS STRUCTURE IS MORE COMPLETE THAN
REMARK 7 THE STARTING MODEL OF THE NATIVE STRUCTURE (PDB ID 2ACE).
REMARK 7 RESIDUES THAT ARE NOT SEEN IN THE CRYSTAL STRUCTURE DUE TO
REMARK 7 DISORDER INCLUDE THE N-TERMINAL RESIDUE ASP 1 AND THE
REMARK 7 C-TERMINAL RESIDUES AFTER THR 535. THR 535 IS THE LAST
REMARK 7 RESIDUE OBSERVED AT THE C-TERMINUS.
REMARK 8
REMARK 8 TER
REMARK 8 THR: THE LAST "VISIBLE" RESIDUE
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-DEC-1998.
REMARK 100 THE RCSB ID CODE IS RCSB000232.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 15-MAY-1998
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 5.80
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 FR300
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : NI FILTER
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42208
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 93.7
REMARK 200 DATA REDUNDANCY : 2.500
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.05000
REMARK 200 FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38
REMARK 200 COMPLETENESS FOR SHELL (%) : 65.2
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
REMARK 200 REPLACEMENT
REMARK 200 SOFTWARE USED: CNS 0.4
REMARK 200 STARTING MODEL: PDB ENTRY 2ACE
REMARK 200
REMARK 200 REMARK: USED COMPOSITE OMIT MAP METHOD
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 68.0
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.80
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 200, MES
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,1/3+Z
REMARK 290 3555 -X+Y,-X,2/3+Z
REMARK 290 4555 Y,X,-Z
REMARK 290 5555 X-Y,-Y,2/3-Z
REMARK 290 6555 -X,-X+Y,1/3-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 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.62700
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 91.25400
REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 91.25400
REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 45.62700
REMARK 290
REMARK 290 REMARK: NULL
REMARK 291
REMARK 291 293
REMARK 295
REMARK 300
REMARK 300 BIOMOLECULE
REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT
REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR
REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).
REMARK 350
REMARK 350 GENERATING THE BIOMOLECULE
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 APPLY THE FOLLOWING TO CHAINS: A, B, C
REMARK 350 BIOMT1 1 -0.500000 0.866025 0.000000 -56.31800
REMARK 350 BIOMT2 1 -0.866025 -0.500000 0.000000 97.54564
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 -45.62700
REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH 2116 LIES ON A SPECIAL POSITION.
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
REMARK 500 O HOH 2057 O HOH 2058 2.13
REMARK 500 O HOH 2082 O HOH 2083 2.18
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 4*RMSD AND BY MORE THAN 0.150 ANGSTROMS (M=MODEL
REMARK 500 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 500 NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,1X,2(A4,A1,3X),12X,F5.3)
REMARK 500
REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991
REMARK 500
REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
REMARK 500 MET A 520 SD MET A 520 CE 0.199
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 4*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: ENGH AND HUBER, 1991
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 HIS A 3 C - N - CA ANGL. DEV. = 8.1 DEGREES
REMARK 500 GLU A 5 N - CA - C ANGL. DEV. = 7.8 DEGREES
REMARK 500 SER A 25 N - CA - C ANGL. DEV. = -7.9 DEGREES
REMARK 500 SER A 55 N - CA - C ANGL. DEV. = -9.2 DEGREES
REMARK 500 VAL A 129 C - CA - CB ANGL. DEV. = -9.5 DEGREES
REMARK 500 LYS A 133 N - CA - C ANGL. DEV. = 8.0 DEGREES
REMARK 500 VAL A 142 N - CA - C ANGL. DEV. =-11.3 DEGREES
REMARK 500 LEU A 143 CA - CB - CG ANGL. DEV. = -9.9 DEGREES
REMARK 500 ASN A 167 N - CA - C ANGL. DEV. = 8.1 DEGREES
REMARK 500 ASN A 183 N - CA - C ANGL. DEV. = 9.0 DEGREES
REMARK 500 SER A 228 C - CA - CB ANGL. DEV. =-10.0 DEGREES
REMARK 500 ALA A 234 N - CA - C ANGL. DEV. = 10.2 DEGREES
REMARK 500 LEU A 248 CA - CB - CG ANGL. DEV. = -9.5 DEGREES
REMARK 500 ASN A 255 N - CA - C ANGL. DEV. = -9.1 DEGREES
REMARK 500 LYS A 270 N - CA - C ANGL. DEV. = -8.9 DEGREES
REMARK 500 LEU A 282 CA - CB - CG ANGL. DEV. = -8.2 DEGREES
REMARK 500 PRO A 283 N - CA - C ANGL. DEV. = 9.7 DEGREES
REMARK 500 ILE A 296 N - CA - C ANGL. DEV. = -9.9 DEGREES
REMARK 500 ASP A 297 N - CA - C ANGL. DEV. = 9.6 DEGREES
REMARK 500 MET A 308 CG - SD - CE ANGL. DEV. = 8.1 DEGREES
REMARK 500 GLY A 328 N - CA - C ANGL. DEV. = 9.4 DEGREES
REMARK 500 SER A 329 N - CA - C ANGL. DEV. = 7.9 DEGREES
REMARK 500 LYS A 346 N - CA - C ANGL. DEV. = -9.8 DEGREES
REMARK 500 ASP A 377 N - CA - C ANGL. DEV. = -9.1 DEGREES
REMARK 500 MET A 379 CG - SD - CE ANGL. DEV. = 8.5 DEGREES
REMARK 500 PHE A 422 N - CA - C ANGL. DEV. = -8.0 DEGREES
REMARK 500 ARG A 426 CB - CG - CD ANGL. DEV. = 9.4 DEGREES
REMARK 500 VAL A 438 N - CA - C ANGL. DEV. = -8.5 DEGREES
REMARK 500 ILE A 439 N - CA - C ANGL. DEV. = 8.6 DEGREES
REMARK 500 GLU A 443 N - CA - C ANGL. DEV. = -8.1 DEGREES
REMARK 500 GLY A 449 N - CA - C ANGL. DEV. = 8.2 DEGREES
REMARK 500 LEU A 452 CA - CB - CG ANGL. DEV. = 8.7 DEGREES
REMARK 500 THR A 479 N - CA - C ANGL. DEV. = 7.8 DEGREES
REMARK 500 TRP A 492 N - CA - C ANGL. DEV. = -8.5 DEGREES
REMARK 500 LEU A 494 CA - CB - CG ANGL. DEV. = 12.9 DEGREES
REMARK 500 PHE A 495 N - CA - C ANGL. DEV. = -9.1 DEGREES
REMARK 500 ASP A 504 N - CA - C ANGL. DEV. =-12.9 DEGREES
REMARK 500 LYS A 511 CD - CE - NZ ANGL. DEV. = 8.5 DEGREES
REMARK 500 LEU A 516 CA - CB - CG ANGL. DEV. = 10.3 DEGREES
REMARK 500 VAL A 518 C - CA - CB ANGL. DEV. = -8.9 DEGREES
REMARK 500 LYS A 530 CD - CE - NZ ANGL. DEV. = 9.0 DEGREES
REMARK 500 LEU A 531 CA - CB - CG ANGL. DEV. = 17.3 DEGREES
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 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500
REMARK 500 HIS A 3 117.93 98.00
REMARK 525
REMARK 525 SOLVENT
REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED
REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE
REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL
REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 0 HOH 2056 DISTANCE = 5.09 ANGSTROMS
REMARK 600
REMARK 600 HETEROGEN
REMARK 600 DFP, AGED ORGANOPHOSPHATE
REMARK 600
REMARK 600 MES, USED AS THE CRYSTALLIZATION BUFFER
REMARK 600
REMARK 600 THERE ARE 5 NAG GROUPS NUMBERED 3001-3005 IN THIS STRUCTURE
REMARK 600
REMARK 650
REMARK 650 HELIX
REMARK 650 DETERMINATION METHOD: TAKEN FROM RELEASED PDB ENTRY 2ACE
REMARK 700
REMARK 700 SHEET
REMARK 700 DETERMINATION METHOD: SHEETTAKEN FROM RELEASED PDB ENTRY
REMARK 700 2ACE
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: CAT
REMARK 800 SITE_DESCRIPTION:
DBREF 2DFP A 2 535 SWS P04058 ACES_TORCA 23 556
SEQRES 1 A 534 ASP HIS SER GLU LEU LEU VAL ASN THR LYS SER GLY LYS
SEQRES 2 A 534 VAL MET GLY THR ARG VAL PRO VAL LEU SER SER HIS ILE
SEQRES 3 A 534 SER ALA PHE LEU GLY ILE PRO PHE ALA GLU PRO PRO VAL
SEQRES 4 A 534 GLY ASN MET ARG PHE ARG ARG PRO GLU PRO LYS LYS PRO
SEQRES 5 A 534 TRP SER GLY VAL TRP ASN ALA SER THR TYR PRO ASN ASN
SEQRES 6 A 534 CYS GLN GLN TYR VAL ASP GLU GLN PHE PRO GLY PHE SER
SEQRES 7 A 534 GLY SER GLU MET TRP ASN PRO ASN ARG GLU MET SER GLU
SEQRES 8 A 534 ASP CYS LEU TYR LEU ASN ILE TRP VAL PRO SER PRO ARG
SEQRES 9 A 534 PRO LYS SER THR THR VAL MET VAL TRP ILE TYR GLY GLY
SEQRES 10 A 534 GLY PHE TYR SER GLY SER SER THR LEU ASP VAL TYR ASN
SEQRES 11 A 534 GLY LYS TYR LEU ALA TYR THR GLU GLU VAL VAL LEU VAL
SEQRES 12 A 534 SER LEU SER TYR ARG VAL GLY ALA PHE GLY PHE LEU ALA
SEQRES 13 A 534 LEU HIS GLY SER GLN GLU ALA PRO GLY ASN VAL GLY LEU
SEQRES 14 A 534 LEU ASP GLN ARG MET ALA LEU GLN TRP VAL HIS ASP ASN
SEQRES 15 A 534 ILE GLN PHE PHE GLY GLY ASP PRO LYS THR VAL THR ILE
SEQRES 16 A 534 PHE GLY GLU MIS ALA GLY GLY ALA SER VAL GLY MET HIS
SEQRES 17 A 534 ILE LEU SER PRO GLY SER ARG ASP LEU PHE ARG ARG ALA
SEQRES 18 A 534 ILE LEU GLN SER GLY SER PRO ASN CYS PRO TRP ALA SER
SEQRES 19 A 534 VAL SER VAL ALA GLU GLY ARG ARG ARG ALA VAL GLU LEU
SEQRES 20 A 534 GLY ARG ASN LEU ASN CYS ASN LEU ASN SER ASP GLU GLU
SEQRES 21 A 534 LEU ILE HIS CYS LEU ARG GLU LYS LYS PRO GLN GLU LEU
SEQRES 22 A 534 ILE ASP VAL GLU TRP ASN VAL LEU PRO PHE ASP SER ILE
SEQRES 23 A 534 PHE ARG PHE SER PHE VAL PRO VAL ILE ASP GLY GLU PHE
SEQRES 24 A 534 PHE PRO THR SER LEU GLU SER MET LEU ASN SER GLY ASN
SEQRES 25 A 534 PHE LYS LYS THR GLN ILE LEU LEU GLY VAL ASN LYS ASP
SEQRES 26 A 534 GLU GLY SER PHE PHE LEU LEU TYR GLY ALA PRO GLY PHE
SEQRES 27 A 534 SER LYS ASP SER GLU SER LYS ILE SER ARG GLU ASP PHE
SEQRES 28 A 534 MET SER GLY VAL LYS LEU SER VAL PRO HIS ALA ASN ASP
SEQRES 29 A 534 LEU GLY LEU ASP ALA VAL THR LEU GLN TYR THR ASP TRP
SEQRES 30 A 534 MET ASP ASP ASN ASN GLY ILE LYS ASN ARG ASP GLY LEU
SEQRES 31 A 534 ASP ASP ILE VAL GLY ASP HIS ASN VAL ILE CYS PRO LEU
SEQRES 32 A 534 MET HIS PHE VAL ASN LYS TYR THR LYS PHE GLY ASN GLY
SEQRES 33 A 534 THR TYR LEU TYR PHE PHE ASN HIS ARG ALA SER ASN LEU
SEQRES 34 A 534 VAL TRP PRO GLU TRP MET GLY VAL ILE HIS GLY TYR GLU
SEQRES 35 A 534 ILE GLU PHE VAL PHE GLY LEU PRO LEU VAL LYS GLU LEU
SEQRES 36 A 534 ASN TYR THR ALA GLU GLU GLU ALA LEU SER ARG ARG ILE
SEQRES 37 A 534 MET HIS TYR TRP ALA THR PHE ALA LYS THR GLY ASN PRO
SEQRES 38 A 534 ASN GLU PRO HIS SER GLN GLU SER LYS TRP PRO LEU PHE
SEQRES 39 A 534 THR THR LYS GLU GLN LYS PHE ILE ASP LEU ASN THR GLU
SEQRES 40 A 534 PRO MET LYS VAL HIS GLN ARG LEU ARG VAL GLN MET CYS
SEQRES 41 A 534 VAL PHE TRP ASN GLN PHE LEU PRO LYS LEU LEU ASN ALA
SEQRES 42 A 534 THR
MODRES 2DFP MIS A 200 SER MONOISOPROPYLPHOSPHORYLSERINE
HET MIS A 200 13
HET NAG B3002 14
HET NAG B3003 14
HET NAG C3004 14
HET NAG C3005 14
HET NAG 3001 14
HET MES 4001 12
HETNAM MIS MONOISOPROPYLPHOSPHORYLSERINE
HETNAM NAG N-ACETYL-D-GLUCOSAMINE
HETNAM MES N-(ETHYLSULFITE)MORPHOLINE
HETSYN NAG NAG
FORMUL 1 MIS C6 H14 N1 O6 P1
FORMUL 2 NAG 5(C8 H15 N1 O6)
FORMUL 5 MES C6 H14 N1 O4 S1
FORMUL 6 HOH *376(H2 O1)
HELIX 1 1 GLY A 41 MET A 43 5 3
HELIX 2 2 SER A 79 GLU A 82 1 4
HELIX 3 3 ASP A 128 TYR A 130 5 3
HELIX 4 4 LYS A 133 GLU A 139 1 7
HELIX 5 5 GLY A 151 PHE A 155 1 5
HELIX 6 6 VAL A 168 ASN A 183 1 16
HELIX 7 7 ILE A 184 PHE A 187 5 4
HELIX 8 8 GLY A 202 LEU A 211 1 10
HELIX 9 9 PRO A 213 ARG A 216 1 4
HELIX 10 10 VAL A 238 ASN A 251 1 14
HELIX 11 11 ASP A 259 GLU A 268 1 10
HELIX 12 12 PRO A 271 VAL A 277 1 7
HELIX 13 13 GLU A 278 ASN A 280 5 3
HELIX 14 14 LEU A 305 SER A 311 1 7
HELIX 15 15 SER A 329 GLY A 335 1 7
HELIX 16 16 ARG A 349 SER A 359 1 11
HELIX 17 17 ASP A 365 TYR A 375 1 11
HELIX 18 18 GLY A 384 ASN A 399 1 16
HELIX 19 19 ILE A 401 PHE A 414 1 14
HELIX 20 20 GLU A 434 MET A 436 5 3
HELIX 21 21 ILE A 444 VAL A 447 1 4
HELIX 22 22 LEU A 450 LEU A 452 5 3
HELIX 23 23 LYS A 454 LEU A 456 5 3
HELIX 24 24 ALA A 460 THR A 479 1 20
HELIX 25 25 VAL A 518 ASN A 525 1 8
HELIX 26 26 PHE A 527 ALA A 534 1 8
SHEET 1 A 3 LEU A 6 THR A 10 0
SHEET 2 A 3 GLY A 13 MET A 16 -1 N VAL A 15 O VAL A 8
SHEET 3 A 3 VAL A 57 ALA A 60 1 N TRP A 58 O LYS A 14
SHEET 1 B11 MET A 16 PRO A 21 0
SHEET 2 B11 HIS A 26 PRO A 34 -1 O ALA A 29 N THR A 18
SHEET 3 B11 TYR A 96 PRO A 102 -1 N ILE A 99 O PHE A 30
SHEET 4 B11 VAL A 142 SER A 147 -1 N LEU A 143 O TRP A 100
SHEET 5 B11 THR A 109 TYR A 116 1 N MET A 112 O VAL A 142
SHEET 6 B11 THR A 193 GLU A 199 1 O THR A 195 N VAL A 113
SHEET 7 B11 ARG A 220 SER A 226 1 N ILE A 223 O ILE A 196
SHEET 8 B11 GLN A 318 ASN A 324 1 N GLY A 322 O LEU A 224
SHEET 9 B11 GLY A 417 PHE A 423 1 N TYR A 421 O LEU A 321
SHEET 10 B11 PHE A 502 LEU A 505 1 N ILE A 503 O LEU A 420
SHEET 11 B11 MET A 510 GLN A 514 -1 N HIS A 513 O PHE A 502
SSBOND 1 CYS A 67 CYS A 94
SSBOND 2 CYS A 254 CYS A 265
SSBOND 3 CYS A 402 CYS A 521
LINK O4 NAG B3002 C1 NAG B3003
LINK O4 NAG C3004 C1 NAG C3005
LINK ND2 ASN A 416 C1 NAG B3002
LINK ND2 ASN A 457 C1 NAG C3004
LINK ND2 ASN A 59 C1 NAG 3001
CISPEP 1 SER A 103 PRO A 104 0 -0.08
SITE 1 CAT 3 MIS A 200 GLU A 327 HIS A 440
SITE 1 OPB 1 MIS A 200
CRYST1 112.636 112.636 136.881 90.00 90.00 120.00 P 31 2 1 6
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 0.008878 0.005126 0.000000 0.00000
SCALE2 0.000000 0.010252 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007306 0.00000 |