HEADER LYASE 17-JAN-07 2OKK
TITLE THE X-RAY CRYSTAL STRUCTURE OF THE 65KDA ISOFORM OF GLUTAMIC ACID
TITLE 2 DECARBOXYLASE (GAD65)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: GLUTAMATE DECARBOXYLASE 2;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: RESIDUES 88-584;
COMPND 5 SYNONYM: GLUTAMATE DECARBOXYLASE 65 KDA ISOFORM, GAD-65, 65 KDA
COMPND 6 GLUTAMIC ACID DECARBOXYLASE;
COMPND 7 EC: 4.1.1.15;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: GAD2, GAD65;
SOURCE 6 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE;
SOURCE 7 EXPRESSION_SYSTEM_COMMON: BAKER'S YEAST;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 4932;
SOURCE 9 EXPRESSION_SYSTEM_STRAIN: YRD-15;
SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PRJ
KEYWDS PLP-DEPENDENT DECARBOXYLASE, LYASE
EXPDTA X-RAY DIFFRACTION
AUTHOR A.M.BUCKLE,G.FENALTI,R.H.P.LAW,J.C.WHISSTOCK
REVDAT 5 13-JUL-11 2OKK 1 VERSN
REVDAT 4 22-SEP-09 2OKK 1 HETATM
REVDAT 3 24-FEB-09 2OKK 1 VERSN
REVDAT 2 24-APR-07 2OKK 1 JRNL
REVDAT 1 27-MAR-07 2OKK 0
JRNL AUTH G.FENALTI,R.H.LAW,A.M.BUCKLE,C.LANGENDORF,K.TUCK,C.J.ROSADO,
JRNL AUTH 2 N.G.FAUX,K.MAHMOOD,C.S.HAMPE,J.P.BANGA,M.WILCE,
JRNL AUTH 3 J.SCHMIDBERGER,J.ROSSJOHN,O.EL-KABBANI,R.N.PIKE,A.I.SMITH,
JRNL AUTH 4 I.R.MACKAY,M.J.ROWLEY,J.C.WHISSTOCK
JRNL TITL GABA PRODUCTION BY GLUTAMIC ACID DECARBOXYLASE IS REGULATED
JRNL TITL 2 BY A DYNAMIC CATALYTIC LOOP.
JRNL REF NAT.STRUCT.MOL.BIOL. V. 14 280 2007
JRNL REFN ISSN 1545-9993
JRNL PMID 17384644
JRNL DOI 10.1038/NSMB1228
REMARK 2
REMARK 2 RESOLUTION. 2.30 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) : 2.30
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.19
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9
REMARK 3 NUMBER OF REFLECTIONS : 20648
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) : 0.200
REMARK 3 R VALUE (WORKING SET) : 0.196
REMARK 3 FREE R VALUE : 0.256
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200
REMARK 3 FREE R VALUE TEST SET COUNT : 1077
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) : 2.30
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1389
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.85
REMARK 3 BIN R VALUE (WORKING SET) : 0.2470
REMARK 3 BIN FREE R VALUE SET COUNT : 66
REMARK 3 BIN FREE R VALUE : 0.3540
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3770
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 20
REMARK 3 SOLVENT ATOMS : 92
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.40
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -1.32000
REMARK 3 B22 (A**2) : 0.94000
REMARK 3 B33 (A**2) : 0.37000
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): 0.454
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.269
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.203
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.110
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.909
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3877 ; 0.009 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5246 ; 1.352 ; 1.965
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 480 ; 5.799 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 156 ;37.868 ;24.038
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 658 ;17.640 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;17.402 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 578 ; 0.129 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2879 ; 0.004 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1811 ; 0.203 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2611 ; 0.303 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 165 ; 0.143 ; 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): 111 ; 0.174 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.117 ; 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): 2463 ; 1.021 ; 2.000
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3849 ; 1.908 ; 5.000
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1629 ; 3.756 ; 7.000
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1397 ; 5.202 ;10.000
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 : BABINET MODEL WITH 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 2OKK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JAN-07.
REMARK 100 THE RCSB ID CODE IS RCSB041251.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 01-APR-06
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.2
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 17-ID
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.000
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA)
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20717
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300
REMARK 200 RESOLUTION RANGE LOW (A) : 37.190
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : NULL
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> 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) : 2.42
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8
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 <I/SIGMA(I)> 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: PHASER
REMARK 200 STARTING MODEL: PDB ENTRY 2OKJ
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 39.91
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 20% ETHANOL, 100 MM MES, 10 MM 2-
REMARK 280 MERCAPTOETHANOL, 20 MM CACL2, PH 6.2, VAPOR DIFFUSION, HANGING
REMARK 280 DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -X,Y,-Z+1/2
REMARK 290 4555 X,-Y,-Z
REMARK 290 5555 X+1/2,Y+1/2,Z
REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2
REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2
REMARK 290 8555 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 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.00450
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.00450
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 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 39.12550
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.52850
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 39.12550
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.52850
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 60.00450
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 39.12550
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.52850
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 60.00450
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 39.12550
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.52850
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
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 300 REMARK: THE BIOLOGICAL UNIT (DIMER) IS GENERATED BY APPLYING
REMARK 300 CRYSTALLOGRAPHIC SYMMETRY.
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,PQS
REMARK 350 TOTAL BURIED SURFACE AREA: 13330 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 31890 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -110.0 KCAL/MOL
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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -60.00450
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 A 596 LIES ON A SPECIAL POSITION.
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 ALA A 423
REMARK 465 SER A 424
REMARK 465 TYR A 425
REMARK 465 LEU A 426
REMARK 465 PHE A 427
REMARK 465 GLN A 428
REMARK 465 GLN A 429
REMARK 465 ASP A 430
REMARK 465 LYS A 431
REMARK 465 HIS A 432
REMARK 465 TYR A 433
REMARK 465 ASP A 518
REMARK 465 ASN A 519
REMARK 465 GLU A 520
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 PHE A 91 CG CD1 CD2 CE1 CE2 CZ
REMARK 470 ASP A 102 CG OD1 OD2
REMARK 470 ARG A 105 CG CD NE CZ NH1 NH2
REMARK 470 GLN A 120 OE1 NE2
REMARK 470 LYS A 124 CD CE NZ
REMARK 470 ASN A 139 CG OD1
REMARK 470 ASP A 151 OD1 OD2
REMARK 470 GLN A 152 CG CD OE1 NE2
REMARK 470 LYS A 303 CD CE NZ
REMARK 470 ARG A 307 CZ NH1 NH2
REMARK 470 HIS A 422 CG ND1 CD2 CE1 NE2
REMARK 470 LEU A 435 CG CD1 CD2
REMARK 470 SER A 436 OG
REMARK 470 TYR A 437 CG CD1 CD2 CE1 CE2 CZ OH
REMARK 470 ARG A 460 NE CZ NH1 NH2
REMARK 470 LYS A 473 CD CE NZ
REMARK 470 GLU A 476 CD OE1 OE2
REMARK 470 THR A 515 OG1 CG2
REMARK 470 GLU A 517 CG CD OE1 OE2
REMARK 470 GLU A 521 CD OE1 OE2
REMARK 470 ARG A 522 CG CD NE CZ NH1 NH2
REMARK 470 MET A 523 CG SD CE
REMARK 470 ARG A 536 CD NE CZ NH1 NH2
REMARK 470 ASP A 584 CG OD1 OD2
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 ASN A 201 66.24 38.81
REMARK 500 ALA A 336 79.64 -101.84
REMARK 500 VAL A 340 -71.00 -94.98
REMARK 500 LLP A 396 -94.81 -84.58
REMARK 500 GLN A 403 80.21 75.74
REMARK 500 THR A 439 -37.44 94.84
REMARK 500 CYS A 446 -86.28 -106.93
REMARK 500 HIS A 501 139.38 111.29
REMARK 500 SER A 512 32.31 -90.40
REMARK 500 LEU A 513 -15.01 -152.87
REMARK 500 ASN A 555 110.41 -29.57
REMARK 500 SER A 562 -4.31 -150.92
REMARK 500 GLN A 583 81.06 -153.76
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 GLN A 500 HIS A 501 -36.58
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 A 205 22.1 L L OUTSIDE RANGE
REMARK 500 GLN A 403 24.0 L L OUTSIDE RANGE
REMARK 500 THR A 439 23.7 L L OUTSIDE RANGE
REMARK 500 GLN A 500 19.3 L L OUTSIDE RANGE
REMARK 500 HIS A 501 7.0 L L EXPECTING SP3
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 ABU A 585
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ABU A 586
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 587
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2OKJ RELATED DB: PDB
DBREF 2OKK A 88 584 UNP Q05329 DCE2_HUMAN 88 584
SEQRES 1 A 497 ASN TYR ALA PHE LEU HIS ALA THR ASP LEU LEU PRO ALA
SEQRES 2 A 497 CYS ASP GLY GLU ARG PRO THR LEU ALA PHE LEU GLN ASP
SEQRES 3 A 497 VAL MET ASN ILE LEU LEU GLN TYR VAL VAL LYS SER PHE
SEQRES 4 A 497 ASP ARG SER THR LYS VAL ILE ASP PHE HIS TYR PRO ASN
SEQRES 5 A 497 GLU LEU LEU GLN GLU TYR ASN TRP GLU LEU ALA ASP GLN
SEQRES 6 A 497 PRO GLN ASN LEU GLU GLU ILE LEU MET HIS CYS GLN THR
SEQRES 7 A 497 THR LEU LYS TYR ALA ILE LYS THR GLY HIS PRO ARG TYR
SEQRES 8 A 497 PHE ASN GLN LEU SER THR GLY LEU ASP MET VAL GLY LEU
SEQRES 9 A 497 ALA ALA ASP TRP LEU THR SER THR ALA ASN THR ASN MET
SEQRES 10 A 497 PHE THR TYR GLU ILE ALA PRO VAL PHE VAL LEU LEU GLU
SEQRES 11 A 497 TYR VAL THR LEU LYS LYS MET ARG GLU ILE ILE GLY TRP
SEQRES 12 A 497 PRO GLY GLY SER GLY ASP GLY ILE PHE SER PRO GLY GLY
SEQRES 13 A 497 ALA ILE SER ASN MET TYR ALA MET MET ILE ALA ARG PHE
SEQRES 14 A 497 LYS MET PHE PRO GLU VAL LYS GLU LYS GLY MET ALA ALA
SEQRES 15 A 497 LEU PRO ARG LEU ILE ALA PHE THR SER GLU HIS SER HIS
SEQRES 16 A 497 PHE SER LEU LYS LYS GLY ALA ALA ALA LEU GLY ILE GLY
SEQRES 17 A 497 THR ASP SER VAL ILE LEU ILE LYS CYS ASP GLU ARG GLY
SEQRES 18 A 497 LYS MET ILE PRO SER ASP LEU GLU ARG ARG ILE LEU GLU
SEQRES 19 A 497 ALA LYS GLN LYS GLY PHE VAL PRO PHE LEU VAL SER ALA
SEQRES 20 A 497 THR ALA GLY THR THR VAL TYR GLY ALA PHE ASP PRO LEU
SEQRES 21 A 497 LEU ALA VAL ALA ASP ILE CYS LYS LYS TYR LYS ILE TRP
SEQRES 22 A 497 MET HIS VAL ASP ALA ALA TRP GLY GLY GLY LEU LEU MET
SEQRES 23 A 497 SER ARG LYS HIS LYS TRP LYS LEU SER GLY VAL GLU ARG
SEQRES 24 A 497 ALA ASN SER VAL THR TRP ASN PRO HIS LLP MET MET GLY
SEQRES 25 A 497 VAL PRO LEU GLN CYS SER ALA LEU LEU VAL ARG GLU GLU
SEQRES 26 A 497 GLY LEU MET GLN ASN CYS ASN GLN MET HIS ALA SER TYR
SEQRES 27 A 497 LEU PHE GLN GLN ASP LYS HIS TYR ASP LEU SER TYR ASP
SEQRES 28 A 497 THR GLY ASP LYS ALA LEU GLN CYS GLY ARG HIS VAL ASP
SEQRES 29 A 497 VAL PHE LYS LEU TRP LEU MET TRP ARG ALA LYS GLY THR
SEQRES 30 A 497 THR GLY PHE GLU ALA HIS VAL ASP LYS CYS LEU GLU LEU
SEQRES 31 A 497 ALA GLU TYR LEU TYR ASN ILE ILE LYS ASN ARG GLU GLY
SEQRES 32 A 497 TYR GLU MET VAL PHE ASP GLY LYS PRO GLN HIS THR ASN
SEQRES 33 A 497 VAL CYS PHE TRP TYR ILE PRO PRO SER LEU ARG THR LEU
SEQRES 34 A 497 GLU ASP ASN GLU GLU ARG MET SER ARG LEU SER LYS VAL
SEQRES 35 A 497 ALA PRO VAL ILE LYS ALA ARG MET MET GLU TYR GLY THR
SEQRES 36 A 497 THR MET VAL SER TYR GLN PRO LEU GLY ASP LYS VAL ASN
SEQRES 37 A 497 PHE PHE ARG MET VAL ILE SER ASN PRO ALA ALA THR HIS
SEQRES 38 A 497 GLN ASP ILE ASP PHE LEU ILE GLU GLU ILE GLU ARG LEU
SEQRES 39 A 497 GLY GLN ASP
MODRES 2OKK LLP A 396 LYS
HET LLP A 396 24
HET ABU A 585 7
HET ABU A 586 7
HET GOL A 587 6
HETNAM LLP 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-
HETNAM 2 LLP PYRIDIN-4-YLMETHANE)
HETNAM ABU GAMMA-AMINO-BUTANOIC ACID
HETNAM GOL GLYCEROL
HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE
HETSYN ABU GAMMA(AMINO)-BUTYRIC ACID
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 1 LLP C14 H24 N3 O7 P
FORMUL 2 ABU 2(C4 H9 N O2)
FORMUL 4 GOL C3 H8 O3
FORMUL 5 HOH *92(H2 O)
HELIX 1 1 ASN A 88 LEU A 92 5 5
HELIX 2 2 HIS A 93 LEU A 97 5 5
HELIX 3 3 GLY A 103 ASP A 127 1 25
HELIX 4 4 TYR A 137 TYR A 145 1 9
HELIX 5 5 ASN A 155 ALA A 170 1 16
HELIX 6 6 ASP A 187 ASN A 201 1 15
HELIX 7 7 ALA A 210 GLY A 229 1 20
HELIX 8 8 TRP A 230 SER A 234 5 5
HELIX 9 9 GLY A 242 PHE A 259 1 18
HELIX 10 10 GLU A 261 GLY A 266 1 6
HELIX 11 11 MET A 267 LEU A 270 5 4
HELIX 12 12 PHE A 283 LEU A 292 1 10
HELIX 13 13 GLY A 295 ASP A 297 5 3
HELIX 14 14 ILE A 311 LYS A 325 1 15
HELIX 15 15 PRO A 346 LYS A 358 1 13
HELIX 16 16 TRP A 367 SER A 374 5 8
HELIX 17 17 HIS A 377 SER A 382 5 6
HELIX 18 18 GLY A 383 ALA A 387 5 5
HELIX 19 19 GLY A 413 GLN A 420 1 8
HELIX 20 20 ASP A 434 ASP A 438 5 5
HELIX 21 21 THR A 439 ALA A 443 5 5
HELIX 22 22 ASP A 451 ASN A 487 1 37
HELIX 23 23 ARG A 522 SER A 527 1 6
HELIX 24 24 LYS A 528 GLY A 541 1 14
HELIX 25 25 THR A 567 GLY A 582 1 16
SHEET 1 A 5 TYR A 178 PHE A 179 0
SHEET 2 A 5 MET A 544 LEU A 550 1 O MET A 544 N PHE A 179
SHEET 3 A 5 LYS A 553 MET A 559 -1 O ARG A 558 N SER A 546
SHEET 4 A 5 VAL A 504 TYR A 508 -1 N VAL A 504 O MET A 559
SHEET 5 A 5 TYR A 491 MET A 493 -1 N GLU A 492 O TRP A 507
SHEET 1 B 7 ASP A 236 SER A 240 0
SHEET 2 B 7 SER A 405 VAL A 409 -1 O VAL A 409 N ASP A 236
SHEET 3 B 7 SER A 389 TRP A 392 -1 N VAL A 390 O LEU A 408
SHEET 4 B 7 TRP A 360 ALA A 365 1 N VAL A 363 O THR A 391
SHEET 5 B 7 VAL A 328 THR A 335 1 N ALA A 334 O ASP A 364
SHEET 6 B 7 LEU A 273 SER A 278 1 N PHE A 276 O SER A 333
SHEET 7 B 7 VAL A 299 ILE A 302 1 O ILE A 302 N THR A 277
LINK C HIS A 395 N LLP A 396 1555 1555 1.33
LINK C LLP A 396 N MET A 397 1555 1555 1.33
CISPEP 1 LEU A 98 PRO A 99 0 11.19
CISPEP 2 ASP A 438 THR A 439 0 5.41
CISPEP 3 GLN A 583 ASP A 584 0 1.45
SITE 1 AC1 6 GLN A 181 LEU A 182 SER A 183 PHE A 205
SITE 2 AC1 6 THR A 339 ARG A 558
SITE 1 AC2 8 GLN A 181 LEU A 182 SER A 183 ASN A 203
SITE 2 AC2 8 HIS A 282 LLP A 396 CYS A 446 HOH A 661
SITE 1 AC3 5 GLU A 279 SER A 281 HIS A 282 PHE A 283
SITE 2 AC3 5 LYS A 286
CRYST1 78.251 99.057 120.009 90.00 90.00 90.00 C 2 2 21 8
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 0.012779 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010095 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008333 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
