HEADER PROTEIN BINDING 10-AUG-16 5SY9
TITLE ATOMIC RESOLUTION STRUCTURE OF E15Q MUTANT HUMAN DJ-1
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROTEIN DEGLYCASE DJ-1;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: DJ-1,ONCOGENE DJ1,PARKINSON DISEASE PROTEIN 7;
COMPND 5 EC: 3.1.2.-,3.5.1.-;
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: PARK7;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B
KEYWDS DJ-1/PFPI SUPERFAMILY OXIDATIVE STRESS NUCLEOPHILE ELBOW, PROTEIN
KEYWDS 2 BINDING
EXPDTA X-RAY DIFFRACTION
AUTHOR M.A.WILSON,J.LIN
REVDAT 6 04-OCT-23 5SY9 1 REMARK
REVDAT 5 25-DEC-19 5SY9 1 REMARK
REVDAT 4 13-SEP-17 5SY9 1 REMARK
REVDAT 3 01-FEB-17 5SY9 1 JRNL
REVDAT 2 04-JAN-17 5SY9 1 JRNL
REVDAT 1 28-DEC-16 5SY9 0
JRNL AUTH J.LIN,E.POZHARSKI,M.A.WILSON
JRNL TITL SHORT CARBOXYLIC ACID-CARBOXYLATE HYDROGEN BONDS CAN HAVE
JRNL TITL 2 FULLY LOCALIZED PROTONS.
JRNL REF BIOCHEMISTRY V. 56 391 2017
JRNL REFN ISSN 1520-4995
JRNL PMID 27989121
JRNL DOI 10.1021/ACS.BIOCHEM.6B00906
REMARK 2
REMARK 2 RESOLUTION. 1.10 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0151
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9
REMARK 3 NUMBER OF REFLECTIONS : 88556
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) : 0.118
REMARK 3 R VALUE (WORKING SET) : 0.118
REMARK 3 FREE R VALUE : 0.137
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.000
REMARK 3 FREE R VALUE TEST SET COUNT : 2751
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) : 1.10
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.13
REMARK 3 REFLECTION IN BIN (WORKING SET) : 5770
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.55
REMARK 3 BIN R VALUE (WORKING SET) : 0.2870
REMARK 3 BIN FREE R VALUE SET COUNT : 174
REMARK 3 BIN FREE R VALUE : 0.3220
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1385
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 20
REMARK 3 SOLVENT ATOMS : 308
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.23
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.35000
REMARK 3 B22 (A**2) : -0.44000
REMARK 3 B33 (A**2) : 0.10000
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): 0.022
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.023
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.015
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.749
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.984
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.976
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1690 ; 0.014 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 1741 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2306 ; 1.821 ; 2.013
REMARK 3 BOND ANGLES OTHERS (DEGREES): 4062 ; 1.046 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 246 ; 6.327 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 62 ;42.483 ;26.129
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 324 ;11.549 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;17.445 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 266 ; 0.117 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1965 ; 0.010 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 322 ; 0.003 ; 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): 873 ; 0.852 ; 0.932
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 872 ; 0.809 ; 0.929
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1119 ; 1.214 ; 1.411
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1120 ; 1.229 ; 1.413
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 817 ; 1.392 ; 1.220
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 817 ; 1.393 ; 1.220
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1173 ; 1.572 ; 1.690
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2198 ; 8.630 ;17.461
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1981 ; 5.384 ;14.005
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): 3431 ; 2.126 ; 3.000
REMARK 3 SPHERICITY; FREE ATOMS (A**2): 42 ;49.608 ; 5.000
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3658 ;13.182 ; 5.000
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 : NULL
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.30
REMARK 3 ION PROBE RADIUS : 1.00
REMARK 3 SHRINKAGE RADIUS : 1.00
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 5SY9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-AUG-16.
REMARK 100 THE DEPOSITION ID IS D_1000223326.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 24-FEB-16
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SSRL
REMARK 200 BEAMLINE : BL9-2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.88
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : RH COATED COLLIMATING MIRROR, K
REMARK 200 -B FOCUSING MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : AIMLESS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 91327
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100
REMARK 200 RESOLUTION RANGE LOW (A) : 37.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1
REMARK 200 DATA REDUNDANCY : 5.100
REMARK 200 R MERGE (I) : 0.07000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12
REMARK 200 COMPLETENESS FOR SHELL (%) : 85.4
REMARK 200 DATA REDUNDANCY IN SHELL : 3.80
REMARK 200 R MERGE FOR SHELL (I) : 1.06600
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.400
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: 1P5F
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 56.52
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 25-28% PEG 4000, 0.1 M TRIS HCL, 0.1 M
REMARK 280 SODIUM CITRATE, PH 8.5, VAPOR DIFFUSION, SITTING DROP,
REMARK 280 TEMPERATURE 298K
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 21.75600
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 21.75600
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 43.13800
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 60.98150
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 43.13800
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 60.98150
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 21.75600
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 43.13800
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 60.98150
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 21.75600
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 43.13800
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 60.98150
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 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR
REMARK 300 CYCLIC POINT SYMMETRY (SCHOENFLIES SYMBOL = C2).
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: 4600 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 15440 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 16.0 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 -21.75600
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 GLY A -2
REMARK 465 SER A -1
REMARK 465 HIS A 0
REMARK 465 ASP A 189
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 O HOH A 526 O HOH A 589 2.18
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 530 O HOH A 530 3554 1.91
REMARK 500 O HOH A 518 O HOH A 518 3554 1.94
REMARK 500 CG2 THR A 140 O HOH A 506 6445 2.14
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 LYS A 89 CD - CE - NZ ANGL. DEV. = 27.1 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 CSD A 106 -106.22 73.19
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A 605 DISTANCE = 6.04 ANGSTROMS
REMARK 525 HOH A 606 DISTANCE = 6.51 ANGSTROMS
REMARK 525 HOH A 607 DISTANCE = 6.87 ANGSTROMS
REMARK 525 HOH A 608 DISTANCE = 6.91 ANGSTROMS
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 202
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 203
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 204
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 205
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5SY6 RELATED DB: PDB
REMARK 900 5SY6 IS WILD-TYPE DJ-1
REMARK 900 RELATED ID: 5SYA RELATED DB: PDB
REMARK 900 RELATED ID: 5SY4 RELATED DB: PDB
DBREF 5SY9 A 1 189 UNP Q99497 PARK7_HUMAN 1 189
SEQADV 5SY9 GLY A -2 UNP Q99497 EXPRESSION TAG
SEQADV 5SY9 SER A -1 UNP Q99497 EXPRESSION TAG
SEQADV 5SY9 HIS A 0 UNP Q99497 EXPRESSION TAG
SEQADV 5SY9 GLN A 15 UNP Q99497 GLU 15 ENGINEERED MUTATION
SEQRES 1 A 192 GLY SER HIS MET ALA SER LYS ARG ALA LEU VAL ILE LEU
SEQRES 2 A 192 ALA LYS GLY ALA GLN GLU MET GLU THR VAL ILE PRO VAL
SEQRES 3 A 192 ASP VAL MET ARG ARG ALA GLY ILE LYS VAL THR VAL ALA
SEQRES 4 A 192 GLY LEU ALA GLY LYS ASP PRO VAL GLN CYS SER ARG ASP
SEQRES 5 A 192 VAL VAL ILE CYS PRO ASP ALA SER LEU GLU ASP ALA LYS
SEQRES 6 A 192 LYS GLU GLY PRO TYR ASP VAL VAL VAL LEU PRO GLY GLY
SEQRES 7 A 192 ASN LEU GLY ALA GLN ASN LEU SER GLU SER ALA ALA VAL
SEQRES 8 A 192 LYS GLU ILE LEU LYS GLU GLN GLU ASN ARG LYS GLY LEU
SEQRES 9 A 192 ILE ALA ALA ILE CSD ALA GLY PRO THR ALA LEU LEU ALA
SEQRES 10 A 192 HIS GLU ILE GLY PHE GLY SER LYS VAL THR THR HIS PRO
SEQRES 11 A 192 LEU ALA LYS ASP LYS MET MET ASN GLY GLY HIS TYR THR
SEQRES 12 A 192 TYR SER GLU ASN ARG VAL GLU LYS ASP GLY LEU ILE LEU
SEQRES 13 A 192 THR SER ARG GLY PRO GLY THR SER PHE GLU PHE ALA LEU
SEQRES 14 A 192 ALA ILE VAL GLU ALA LEU ASN GLY LYS GLU VAL ALA ALA
SEQRES 15 A 192 GLN VAL LYS ALA PRO LEU VAL LEU LYS ASP
MODRES 5SY9 CSD A 106 CYS MODIFIED RESIDUE
HET CSD A 106 8
HET EDO A 201 8
HET EDO A 202 8
HET EDO A 203 8
HET EDO A 204 4
HET EDO A 205 4
HETNAM CSD 3-SULFINOALANINE
HETNAM EDO 1,2-ETHANEDIOL
HETSYN CSD S-CYSTEINESULFINIC ACID; S-SULFINOCYSTEINE
HETSYN EDO ETHYLENE GLYCOL
FORMUL 1 CSD C3 H7 N O4 S
FORMUL 2 EDO 5(C2 H6 O2)
FORMUL 7 HOH *308(H2 O)
HELIX 1 AA1 GLN A 15 ALA A 29 1 15
HELIX 2 AA2 LEU A 58 LYS A 62 1 5
HELIX 3 AA3 LYS A 63 GLY A 65 5 3
HELIX 4 AA4 GLY A 75 SER A 85 1 11
HELIX 5 AA5 SER A 85 ARG A 98 1 14
HELIX 6 AA6 GLY A 108 HIS A 115 1 8
HELIX 7 AA7 HIS A 126 LEU A 128 5 3
HELIX 8 AA8 ALA A 129 ASN A 135 1 7
HELIX 9 AA9 GLY A 157 GLY A 159 5 3
HELIX 10 AB1 THR A 160 GLY A 174 1 15
HELIX 11 AB2 GLY A 174 ALA A 183 1 10
HELIX 12 AB3 PRO A 184 VAL A 186 5 3
SHEET 1 AA1 7 ALA A 56 SER A 57 0
SHEET 2 AA1 7 LYS A 32 GLY A 37 1 N GLY A 37 O ALA A 56
SHEET 3 AA1 7 ARG A 5 LEU A 10 1 N LEU A 10 O ALA A 36
SHEET 4 AA1 7 VAL A 69 LEU A 72 1 O VAL A 71 N LEU A 7
SHEET 5 AA1 7 LEU A 101 ILE A 105 1 O ALA A 103 N LEU A 72
SHEET 6 AA1 7 ILE A 152 SER A 155 1 O LEU A 153 N ILE A 102
SHEET 7 AA1 7 VAL A 146 ASP A 149 -1 N GLU A 147 O THR A 154
SHEET 1 AA2 2 VAL A 44 GLN A 45 0
SHEET 2 AA2 2 VAL A 51 ILE A 52 -1 O ILE A 52 N VAL A 44
SHEET 1 AA3 2 LYS A 122 VAL A 123 0
SHEET 2 AA3 2 THR A 140 TYR A 141 1 O THR A 140 N VAL A 123
SSBOND 1 CYS A 53 CYS A 53 1555 3554 2.73
LINK C ILE A 105 N CSD A 106 1555 1555 1.35
LINK C CSD A 106 N ALA A 107 1555 1555 1.40
CISPEP 1 GLY A 65 PRO A 66 0 16.89
CISPEP 2 GLY A 65 PRO A 66 0 -11.48
SITE 1 AC1 8 GLY A 65 PRO A 66 TYR A 67 ILE A 91
SITE 2 AC1 8 GLU A 94 GLN A 95 HOH A 318 HOH A 326
SITE 1 AC2 10 GLY A 137 HIS A 138 TYR A 139 THR A 140
SITE 2 AC2 10 LYS A 148 GLU A 170 ALA A 171 HOH A 310
SITE 3 AC2 10 HOH A 390 HOH A 491
SITE 1 AC3 9 ARG A 28 CSD A 106 HIS A 126 PRO A 158
SITE 2 AC3 9 PRO A 184 EDO A 205 HOH A 301 HOH A 371
SITE 3 AC3 9 HOH A 414
SITE 1 AC4 4 GLU A 116 PHE A 119 HOH A 321 HOH A 354
SITE 1 AC5 3 ASN A 76 EDO A 203 HOH A 454
CRYST1 86.276 121.963 43.512 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 0.011591 0.000000 0.000000 0.00000
SCALE2 0.000000 0.008199 0.000000 0.00000
SCALE3 0.000000 0.000000 0.022982 0.00000
(ATOM LINES ARE NOT SHOWN.)
END