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 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 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