HEADER HYDROLASE 31-OCT-13 4NFR
TITLE HUMAN BRAIN ASPARTOACYLASE MUTANT E285A COMPLEX WITH INTERMEDIATE
TITLE 2 ANALOG (N-PHOSPHONOMETHYL-L-ASPARTATE)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ASPARTOACYLASE;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: AMINOACYLASE-2, ACY-2;
COMPND 5 EC: 3.5.1.15;
COMPND 6 ENGINEERED: YES;
COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: ACY2, ASP, ASPA;
SOURCE 6 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS;
SOURCE 7 EXPRESSION_SYSTEM_COMMON: PICHIA PASTORIS;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 4922;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPICZA
KEYWDS CANAVAN DISEASE, N-ACETYL-L-ASPARTATE, ZINC-DEPENDENT HYDROLASE,
KEYWDS 2 ASPARTOACYLASE FAMILY, AMINOACYLASE-2, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.S.WIJAYASINGHE,A.G.PAVLOVSKY,R.E.VIOLA
REVDAT 4 20-SEP-23 4NFR 1 REMARK SEQADV LINK
REVDAT 3 15-NOV-17 4NFR 1 REMARK
REVDAT 2 20-AUG-14 4NFR 1 JRNL
REVDAT 1 30-JUL-14 4NFR 0
JRNL AUTH Y.S.WIJAYASINGHE,A.G.PAVLOVSKY,R.E.VIOLA
JRNL TITL ASPARTOACYLASE CATALYTIC DEFICIENCY AS THE CAUSE OF CANAVAN
JRNL TITL 2 DISEASE: A STRUCTURAL PERSPECTIVE.
JRNL REF BIOCHEMISTRY V. 53 4970 2014
JRNL REFN ISSN 0006-2960
JRNL PMID 25003821
JRNL DOI 10.1021/BI500719K
REMARK 2
REMARK 2 RESOLUTION. 3.00 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.7.0032
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.76
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 73.8
REMARK 3 NUMBER OF REFLECTIONS : 16360
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) : 0.193
REMARK 3 R VALUE (WORKING SET) : 0.191
REMARK 3 FREE R VALUE : 0.241
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 886
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) : 3.00
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08
REMARK 3 REFLECTION IN BIN (WORKING SET) : 242
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 15.29
REMARK 3 BIN R VALUE (WORKING SET) : 0.2800
REMARK 3 BIN FREE R VALUE SET COUNT : 16
REMARK 3 BIN FREE R VALUE : 0.4320
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4834
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 28
REMARK 3 SOLVENT ATOMS : 33
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 49.80
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 72.21
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 3.64000
REMARK 3 B22 (A**2) : 3.64000
REMARK 3 B33 (A**2) : -7.28000
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): 0.445
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.288
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.388
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.934
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.890
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4980 ; 0.007 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 4766 ; 0.003 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6752 ; 1.148 ; 1.970
REMARK 3 BOND ANGLES OTHERS (DEGREES): 11010 ; 0.897 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 600 ; 5.899 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 232 ;36.696 ;24.397
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 866 ;18.245 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;22.948 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 738 ; 0.062 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5568 ; 0.005 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 1120 ; 0.002 ; 0.020
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): 2412 ; 3.281 ; 7.019
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2413 ; 3.280 ; 7.020
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3008 ; 5.387 ;10.520
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3008 ; 5.381 ;10.520
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2568 ; 3.241 ; 7.452
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2569 ; 3.240 ; 7.454
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3745 ; 5.538 ;11.014
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5406 ; 8.661 ;55.168
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5404 ; 8.627 ;55.162
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 NCS TYPE: LOCAL
REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1
REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT
REMARK 3 1 A 10 310 B 10 310 18108 0.12 0.05
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 4NFR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-DEC-13.
REMARK 100 THE DEPOSITION ID IS D_1000083146.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 29-JUL-13
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 23-ID-D
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934
REMARK 200 MONOCHROMATOR : MONOCHROMATOR
REMARK 200 OPTICS : KIRKPATRICK-BAEZ MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17286
REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 90.0
REMARK 200 DATA REDUNDANCY : 2.600
REMARK 200 R MERGE (I) : 0.10100
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.4000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11
REMARK 200 COMPLETENESS FOR SHELL (%) : 90.0
REMARK 200 DATA REDUNDANCY IN SHELL : 1.30
REMARK 200 R MERGE FOR SHELL (I) : 0.18800
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS
REMARK 200 SOFTWARE USED: CCP4
REMARK 200 STARTING MODEL: PDB ENTRY 2O4H
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 68.64
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.92
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG 3350, 0.05M SODIUM CITRATE,
REMARK 280 0.3M POTASSIUM PHOSPHATE (DIBASIC), 3% ETHYLENE GLYCOL, 0.01M
REMARK 280 DTT, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z
REMARK 290 3555 -Y+1/2,X+1/2,Z+1/2
REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2
REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2
REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 -Y,-X,-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 0.00000
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 73.86800
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 73.86800
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 51.36900
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 73.86800
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 73.86800
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 51.36900
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 73.86800
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 73.86800
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 51.36900
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 73.86800
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 73.86800
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 51.36900
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
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 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: 2330 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 25220 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 601 LIES ON A SPECIAL POSITION.
REMARK 375 HOH B 606 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 MET A 1
REMARK 465 THR A 2
REMARK 465 SER A 3
REMARK 465 CYS A 4
REMARK 465 HIS A 5
REMARK 465 ILE A 6
REMARK 465 ALA A 7
REMARK 465 GLU A 8
REMARK 465 GLU A 9
REMARK 465 CYS A 311
REMARK 465 LEU A 312
REMARK 465 HIS A 313
REMARK 465 MET B 1
REMARK 465 THR B 2
REMARK 465 SER B 3
REMARK 465 CYS B 4
REMARK 465 HIS B 5
REMARK 465 ILE B 6
REMARK 465 ALA B 7
REMARK 465 GLU B 8
REMARK 465 GLU B 9
REMARK 465 CYS B 311
REMARK 465 LEU B 312
REMARK 465 HIS B 313
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 OAD AS9 A 501 ZN ZN A 502 1.62
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 GLN A 12 -58.04 -120.22
REMARK 500 TYR A 164 95.72 -173.52
REMARK 500 GLN A 250 45.16 -102.62
REMARK 500 TRP A 252 -18.04 75.26
REMARK 500 MET A 261 -60.51 -121.44
REMARK 500 ILE B 65 -63.25 -90.40
REMARK 500 SER B 161 -20.90 128.12
REMARK 500 LEU B 162 -152.87 -107.81
REMARK 500 LYS B 163 130.76 73.38
REMARK 500 GLN B 250 45.81 -103.49
REMARK 500 TRP B 252 -18.27 74.45
REMARK 500 MET B 261 -60.59 -121.54
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 309 CYS B 310 141.66
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 502 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 21 ND1
REMARK 620 2 GLU A 24 OE1 91.0
REMARK 620 3 HIS A 116 ND1 96.8 85.8
REMARK 620 N 1 2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN B 502 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS B 21 ND1
REMARK 620 2 GLU B 24 OE1 83.4
REMARK 620 3 HIS B 116 ND1 89.2 72.0
REMARK 620 4 AS9 B 501 OAD 148.7 126.7 107.0
REMARK 620 5 AS9 B 501 OAG 88.7 129.8 157.7 66.0
REMARK 620 N 1 2 3 4
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AS9 A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AS9 B 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 502
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2O4H RELATED DB: PDB
REMARK 900 RELATED ID: 2O53 RELATED DB: PDB
DBREF 4NFR A 1 313 UNP P45381 ACY2_HUMAN 1 313
DBREF 4NFR B 1 313 UNP P45381 ACY2_HUMAN 1 313
SEQADV 4NFR ALA A 285 UNP P45381 GLU 285 ENGINEERED MUTATION
SEQADV 4NFR ALA B 285 UNP P45381 GLU 285 ENGINEERED MUTATION
SEQRES 1 A 313 MET THR SER CYS HIS ILE ALA GLU GLU HIS ILE GLN LYS
SEQRES 2 A 313 VAL ALA ILE PHE GLY GLY THR HIS GLY ASN GLU LEU THR
SEQRES 3 A 313 GLY VAL PHE LEU VAL LYS HIS TRP LEU GLU ASN GLY ALA
SEQRES 4 A 313 GLU ILE GLN ARG THR GLY LEU GLU VAL LYS PRO PHE ILE
SEQRES 5 A 313 THR ASN PRO ARG ALA VAL LYS LYS CYS THR ARG TYR ILE
SEQRES 6 A 313 ASP CYS ASP LEU ASN ARG ILE PHE ASP LEU GLU ASN LEU
SEQRES 7 A 313 GLY LYS LYS MET SER GLU ASP LEU PRO TYR GLU VAL ARG
SEQRES 8 A 313 ARG ALA GLN GLU ILE ASN HIS LEU PHE GLY PRO LYS ASP
SEQRES 9 A 313 SER GLU ASP SER TYR ASP ILE ILE PHE ASP LEU HIS ASN
SEQRES 10 A 313 THR THR SER ASN MET GLY CYS THR LEU ILE LEU GLU ASP
SEQRES 11 A 313 SER ARG ASN ASN PHE LEU ILE GLN MET PHE HIS TYR ILE
SEQRES 12 A 313 LYS THR SER LEU ALA PRO LEU PRO CYS TYR VAL TYR LEU
SEQRES 13 A 313 ILE GLU HIS PRO SER LEU LYS TYR ALA THR THR ARG SER
SEQRES 14 A 313 ILE ALA LYS TYR PRO VAL GLY ILE GLU VAL GLY PRO GLN
SEQRES 15 A 313 PRO GLN GLY VAL LEU ARG ALA ASP ILE LEU ASP GLN MET
SEQRES 16 A 313 ARG LYS MET ILE LYS HIS ALA LEU ASP PHE ILE HIS HIS
SEQRES 17 A 313 PHE ASN GLU GLY LYS GLU PHE PRO PRO CYS ALA ILE GLU
SEQRES 18 A 313 VAL TYR LYS ILE ILE GLU LYS VAL ASP TYR PRO ARG ASP
SEQRES 19 A 313 GLU ASN GLY GLU ILE ALA ALA ILE ILE HIS PRO ASN LEU
SEQRES 20 A 313 GLN ASP GLN ASP TRP LYS PRO LEU HIS PRO GLY ASP PRO
SEQRES 21 A 313 MET PHE LEU THR LEU ASP GLY LYS THR ILE PRO LEU GLY
SEQRES 22 A 313 GLY ASP CYS THR VAL TYR PRO VAL PHE VAL ASN ALA ALA
SEQRES 23 A 313 ALA TYR TYR GLU LYS LYS GLU ALA PHE ALA LYS THR THR
SEQRES 24 A 313 LYS LEU THR LEU ASN ALA LYS SER ILE ARG CYS CYS LEU
SEQRES 25 A 313 HIS
SEQRES 1 B 313 MET THR SER CYS HIS ILE ALA GLU GLU HIS ILE GLN LYS
SEQRES 2 B 313 VAL ALA ILE PHE GLY GLY THR HIS GLY ASN GLU LEU THR
SEQRES 3 B 313 GLY VAL PHE LEU VAL LYS HIS TRP LEU GLU ASN GLY ALA
SEQRES 4 B 313 GLU ILE GLN ARG THR GLY LEU GLU VAL LYS PRO PHE ILE
SEQRES 5 B 313 THR ASN PRO ARG ALA VAL LYS LYS CYS THR ARG TYR ILE
SEQRES 6 B 313 ASP CYS ASP LEU ASN ARG ILE PHE ASP LEU GLU ASN LEU
SEQRES 7 B 313 GLY LYS LYS MET SER GLU ASP LEU PRO TYR GLU VAL ARG
SEQRES 8 B 313 ARG ALA GLN GLU ILE ASN HIS LEU PHE GLY PRO LYS ASP
SEQRES 9 B 313 SER GLU ASP SER TYR ASP ILE ILE PHE ASP LEU HIS ASN
SEQRES 10 B 313 THR THR SER ASN MET GLY CYS THR LEU ILE LEU GLU ASP
SEQRES 11 B 313 SER ARG ASN ASN PHE LEU ILE GLN MET PHE HIS TYR ILE
SEQRES 12 B 313 LYS THR SER LEU ALA PRO LEU PRO CYS TYR VAL TYR LEU
SEQRES 13 B 313 ILE GLU HIS PRO SER LEU LYS TYR ALA THR THR ARG SER
SEQRES 14 B 313 ILE ALA LYS TYR PRO VAL GLY ILE GLU VAL GLY PRO GLN
SEQRES 15 B 313 PRO GLN GLY VAL LEU ARG ALA ASP ILE LEU ASP GLN MET
SEQRES 16 B 313 ARG LYS MET ILE LYS HIS ALA LEU ASP PHE ILE HIS HIS
SEQRES 17 B 313 PHE ASN GLU GLY LYS GLU PHE PRO PRO CYS ALA ILE GLU
SEQRES 18 B 313 VAL TYR LYS ILE ILE GLU LYS VAL ASP TYR PRO ARG ASP
SEQRES 19 B 313 GLU ASN GLY GLU ILE ALA ALA ILE ILE HIS PRO ASN LEU
SEQRES 20 B 313 GLN ASP GLN ASP TRP LYS PRO LEU HIS PRO GLY ASP PRO
SEQRES 21 B 313 MET PHE LEU THR LEU ASP GLY LYS THR ILE PRO LEU GLY
SEQRES 22 B 313 GLY ASP CYS THR VAL TYR PRO VAL PHE VAL ASN ALA ALA
SEQRES 23 B 313 ALA TYR TYR GLU LYS LYS GLU ALA PHE ALA LYS THR THR
SEQRES 24 B 313 LYS LEU THR LEU ASN ALA LYS SER ILE ARG CYS CYS LEU
SEQRES 25 B 313 HIS
HET AS9 A 501 13
HET ZN A 502 1
HET AS9 B 501 13
HET ZN B 502 1
HETNAM AS9 N-[HYDROXY(METHYL)PHOSPHORYL]-L-ASPARTIC ACID
HETNAM ZN ZINC ION
HETSYN AS9 N-PHOSPHONOMETHYL-L-ASPARTIC ACID; (2S)-2-
HETSYN 2 AS9 (HYDROPEROXY(METHOXY)PHOSPHORYLAMINO)SUCCINIC ACID
FORMUL 3 AS9 2(C5 H10 N O6 P)
FORMUL 4 ZN 2(ZN 2+)
FORMUL 7 HOH *33(H2 O)
HELIX 1 1 GLU A 24 ASN A 37 1 14
HELIX 2 2 GLY A 38 GLN A 42 5 5
HELIX 3 3 ASN A 54 LYS A 60 1 7
HELIX 4 4 ASP A 68 ILE A 72 5 5
HELIX 5 5 ASP A 74 GLY A 79 1 6
HELIX 6 6 PRO A 87 GLY A 101 1 15
HELIX 7 7 ASN A 133 ALA A 148 1 16
HELIX 8 8 THR A 166 ALA A 171 5 6
HELIX 9 9 ARG A 188 GLU A 211 1 24
HELIX 10 10 ALA A 285 GLU A 290 1 6
HELIX 11 11 GLU B 24 ASN B 37 1 14
HELIX 12 12 GLY B 38 GLN B 42 5 5
HELIX 13 13 ASN B 54 LYS B 60 1 7
HELIX 14 14 ASP B 68 ILE B 72 5 5
HELIX 15 15 ASP B 74 GLY B 79 1 6
HELIX 16 16 PRO B 87 GLY B 101 1 15
HELIX 17 17 ASN B 133 ALA B 148 1 16
HELIX 18 18 THR B 166 ALA B 171 5 6
HELIX 19 19 ARG B 188 GLU B 211 1 24
HELIX 20 20 ALA B 285 GLU B 290 1 6
SHEET 1 A 9 GLU A 47 ILE A 52 0
SHEET 2 A 9 LYS A 13 GLY A 18 1 N ILE A 16 O LYS A 49
SHEET 3 A 9 ILE A 111 ASN A 117 1 O PHE A 113 N PHE A 17
SHEET 4 A 9 TYR A 173 GLY A 180 1 O VAL A 175 N ILE A 112
SHEET 5 A 9 GLY A 123 LEU A 128 -1 N THR A 125 O GLU A 178
SHEET 6 A 9 CYS A 152 LEU A 156 1 O TYR A 153 N LEU A 126
SHEET 7 A 9 CYS A 218 ASP A 230 1 O TYR A 223 N LEU A 156
SHEET 8 A 9 GLU A 293 ALA A 305 -1 O ALA A 294 N VAL A 229
SHEET 9 A 9 TYR A 279 VAL A 281 -1 N VAL A 281 O ALA A 296
SHEET 1 B 3 ILE A 242 ILE A 243 0
SHEET 2 B 3 PRO A 260 LEU A 263 -1 O LEU A 263 N ILE A 242
SHEET 3 B 3 THR A 269 PRO A 271 -1 O ILE A 270 N MET A 261
SHEET 1 C 9 GLU B 47 ILE B 52 0
SHEET 2 C 9 LYS B 13 GLY B 18 1 N VAL B 14 O LYS B 49
SHEET 3 C 9 ILE B 111 ASN B 117 1 O PHE B 113 N PHE B 17
SHEET 4 C 9 TYR B 173 GLY B 180 1 O VAL B 175 N ILE B 112
SHEET 5 C 9 GLY B 123 LEU B 128 -1 N THR B 125 O GLU B 178
SHEET 6 C 9 CYS B 152 LEU B 156 1 O TYR B 153 N LEU B 126
SHEET 7 C 9 CYS B 218 ASP B 230 1 O TYR B 223 N LEU B 156
SHEET 8 C 9 GLU B 293 ALA B 305 -1 O LEU B 301 N VAL B 222
SHEET 9 C 9 TYR B 279 VAL B 281 -1 N VAL B 281 O ALA B 296
SHEET 1 D 3 ILE B 242 ILE B 243 0
SHEET 2 D 3 PRO B 260 LEU B 263 -1 O LEU B 263 N ILE B 242
SHEET 3 D 3 THR B 269 PRO B 271 -1 O ILE B 270 N MET B 261
LINK ND1 HIS A 21 ZN ZN A 502 1555 1555 2.48
LINK OE1 GLU A 24 ZN ZN A 502 1555 1555 2.06
LINK ND1 HIS A 116 ZN ZN A 502 1555 1555 2.20
LINK ND1 HIS B 21 ZN ZN B 502 1555 1555 2.51
LINK OE1 GLU B 24 ZN ZN B 502 1555 1555 2.43
LINK ND1 HIS B 116 ZN ZN B 502 1555 1555 2.49
LINK OAD AS9 B 501 ZN ZN B 502 1555 1555 1.99
LINK OAG AS9 B 501 ZN ZN B 502 1555 1555 2.52
CISPEP 1 GLY A 101 PRO A 102 0 -4.77
CISPEP 2 ALA A 148 PRO A 149 0 9.02
CISPEP 3 GLY A 180 PRO A 181 0 -2.60
CISPEP 4 GLY B 101 PRO B 102 0 -3.74
CISPEP 5 ALA B 148 PRO B 149 0 6.86
CISPEP 6 GLY B 180 PRO B 181 0 -0.98
CISPEP 7 ASP B 266 GLY B 267 0 10.07
SITE 1 AC1 10 HIS A 21 GLU A 24 ARG A 63 ASN A 70
SITE 2 AC1 10 HIS A 116 ASN A 117 TYR A 164 GLU A 178
SITE 3 AC1 10 TYR A 288 ZN A 502
SITE 1 AC2 4 HIS A 21 GLU A 24 HIS A 116 AS9 A 501
SITE 1 AC3 11 HIS B 21 GLU B 24 ARG B 63 ASP B 68
SITE 2 AC3 11 ASN B 70 HIS B 116 TYR B 164 ARG B 168
SITE 3 AC3 11 GLU B 178 ZN B 502 HOH B 611
SITE 1 AC4 4 HIS B 21 GLU B 24 HIS B 116 AS9 B 501
CRYST1 147.736 147.736 102.738 90.00 90.00 90.00 P 42 21 2 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 0.006769 0.000000 0.000000 0.00000
SCALE2 0.000000 0.006769 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009733 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
