HEADER PROTEIN BINDING 23-AUG-07 2R1U TITLE DJ-1 ACTIVATION BY CATECHOL QUINONE MODIFICATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN DJ-1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ONCOGENE DJ1, PARKINSON DISEASE PROTEIN 7; COMPND 5 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: PARK7; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: B834; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET KEYWDS DJ-1, CATECHOL QUINONE, ISOPEPTIDASE, CHAPERONE, CYTOPLASM, DISEASE KEYWDS 2 MUTATION, NUCLEUS, ONCOGENE, OXIDATION, PARKINSON DISEASE, KEYWDS 3 PHOSPHORYLATION, POLYMORPHISM, UBL CONJUGATION, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR Z.ZHONGTAO,F.YUE REVDAT 3 24-JAN-18 2R1U 1 SOURCE AUTHOR JRNL REVDAT 2 24-FEB-09 2R1U 1 VERSN REVDAT 1 26-AUG-08 2R1U 0 JRNL AUTH Z.ZHONGTAO,F.YUE JRNL TITL DJ-1 ACTIVATION BY CATECHOL QUINONE MODIFICATION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.68 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 71845 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.400 REMARK 3 FREE R VALUE TEST SET COUNT : 7230 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2752 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 416 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.94300 REMARK 3 B22 (A**2) : -0.94300 REMARK 3 B33 (A**2) : 1.88600 REMARK 3 B12 (A**2) : -0.87400 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.316 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.946 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.512 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.037 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.010 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 63.55 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 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2R1U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-SEP-07. REMARK 100 THE DEPOSITION ID IS D_1000044319. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 71845 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 500.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 40.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.04000 REMARK 200 R SYM FOR SHELL (I) : 0.04000 REMARK 200 FOR SHELL : 40.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 29%PEG4K, PH 6.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 25.01500 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 50.03000 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: 2800 ANGSTROM**2 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 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 CYS A 106 -108.62 64.91 REMARK 500 CYS B 106 -107.78 65.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1J42 RELATED DB: PDB REMARK 900 RELATED ID: 2R1T RELATED DB: PDB REMARK 900 RELATED ID: 2R1V RELATED DB: PDB DBREF 2R1U A 2 188 UNP Q99497 PARK7_HUMAN 2 188 DBREF 2R1U B 2 188 UNP Q99497 PARK7_HUMAN 2 188 SEQRES 1 A 187 ALA SER LYS ARG ALA LEU VAL ILE LEU ALA LYS GLY ALA SEQRES 2 A 187 GLU GLU MET GLU THR VAL ILE PRO VAL ASP VAL MET ARG SEQRES 3 A 187 ARG ALA GLY ILE LYS VAL THR VAL ALA GLY LEU ALA GLY SEQRES 4 A 187 LYS ASP PRO VAL GLN CYS SER ARG ASP VAL VAL ILE CYS SEQRES 5 A 187 PRO ASP ALA SER LEU GLU ASP ALA LYS LYS GLU GLY PRO SEQRES 6 A 187 TYR ASP VAL VAL VAL LEU PRO GLY GLY ASN LEU GLY ALA SEQRES 7 A 187 GLN ASN LEU SER GLU SER ALA ALA VAL LYS GLU ILE LEU SEQRES 8 A 187 LYS GLU GLN GLU ASN ARG LYS GLY LEU ILE ALA ALA ILE SEQRES 9 A 187 CYS ALA GLY PRO THR ALA LEU LEU ALA HIS GLU ILE GLY SEQRES 10 A 187 PHE GLY SER LYS VAL THR THR HIS PRO LEU ALA LYS ASP SEQRES 11 A 187 LYS MET MET ASN GLY GLY HIS TYR THR TYR SER GLU ASN SEQRES 12 A 187 ARG VAL GLU LYS ASP GLY LEU ILE LEU THR SER ARG GLY SEQRES 13 A 187 PRO GLY THR SER PHE GLU PHE ALA LEU ALA ILE VAL GLU SEQRES 14 A 187 ALA LEU ASN GLY LYS GLU VAL ALA ALA GLN VAL LYS ALA SEQRES 15 A 187 PRO LEU VAL LEU LYS SEQRES 1 B 187 ALA SER LYS ARG ALA LEU VAL ILE LEU ALA LYS GLY ALA SEQRES 2 B 187 GLU GLU MET GLU THR VAL ILE PRO VAL ASP VAL MET ARG SEQRES 3 B 187 ARG ALA GLY ILE LYS VAL THR VAL ALA GLY LEU ALA GLY SEQRES 4 B 187 LYS ASP PRO VAL GLN CYS SER ARG ASP VAL VAL ILE CYS SEQRES 5 B 187 PRO ASP ALA SER LEU GLU ASP ALA LYS LYS GLU GLY PRO SEQRES 6 B 187 TYR ASP VAL VAL VAL LEU PRO GLY GLY ASN LEU GLY ALA SEQRES 7 B 187 GLN ASN LEU SER GLU SER ALA ALA VAL LYS GLU ILE LEU SEQRES 8 B 187 LYS GLU GLN GLU ASN ARG LYS GLY LEU ILE ALA ALA ILE SEQRES 9 B 187 CYS ALA GLY PRO THR ALA LEU LEU ALA HIS GLU ILE GLY SEQRES 10 B 187 PHE GLY SER LYS VAL THR THR HIS PRO LEU ALA LYS ASP SEQRES 11 B 187 LYS MET MET ASN GLY GLY HIS TYR THR TYR SER GLU ASN SEQRES 12 B 187 ARG VAL GLU LYS ASP GLY LEU ILE LEU THR SER ARG GLY SEQRES 13 B 187 PRO GLY THR SER PHE GLU PHE ALA LEU ALA ILE VAL GLU SEQRES 14 B 187 ALA LEU ASN GLY LYS GLU VAL ALA ALA GLN VAL LYS ALA SEQRES 15 B 187 PRO LEU VAL LEU LYS FORMUL 3 HOH *416(H2 O) HELIX 1 1 GLU A 15 ALA A 29 1 15 HELIX 2 2 LEU A 58 LYS A 63 1 6 HELIX 3 3 GLY A 75 SER A 85 1 11 HELIX 4 4 SER A 85 ARG A 98 1 14 HELIX 5 5 PRO A 109 HIS A 115 1 7 HELIX 6 6 HIS A 126 LEU A 128 5 3 HELIX 7 7 ALA A 129 MET A 134 1 6 HELIX 8 8 GLY A 157 GLY A 159 5 3 HELIX 9 9 THR A 160 GLY A 174 1 15 HELIX 10 10 GLY A 174 ALA A 183 1 10 HELIX 11 11 PRO A 184 VAL A 186 5 3 HELIX 12 12 GLU B 15 ALA B 29 1 15 HELIX 13 13 LEU B 58 LYS B 63 1 6 HELIX 14 14 GLY B 75 GLU B 84 1 10 HELIX 15 15 SER B 85 ARG B 98 1 14 HELIX 16 16 PRO B 109 HIS B 115 1 7 HELIX 17 17 HIS B 126 LEU B 128 5 3 HELIX 18 18 ALA B 129 MET B 134 1 6 HELIX 19 19 GLY B 157 GLY B 159 5 3 HELIX 20 20 THR B 160 GLY B 174 1 15 HELIX 21 21 GLY B 174 ALA B 183 1 10 HELIX 22 22 PRO B 184 VAL B 186 5 3 SHEET 1 A 7 ALA A 56 SER A 57 0 SHEET 2 A 7 LYS A 32 GLY A 37 1 N GLY A 37 O ALA A 56 SHEET 3 A 7 ARG A 5 LEU A 10 1 N LEU A 10 O ALA A 36 SHEET 4 A 7 VAL A 69 LEU A 72 1 O VAL A 71 N LEU A 7 SHEET 5 A 7 LEU A 101 ILE A 105 1 O ALA A 103 N LEU A 72 SHEET 6 A 7 ILE A 152 SER A 155 1 O LEU A 153 N ILE A 102 SHEET 7 A 7 VAL A 146 ASP A 149 -1 N GLU A 147 O THR A 154 SHEET 1 B 4 VAL A 44 GLN A 45 0 SHEET 2 B 4 VAL A 51 CYS A 53 -1 O ILE A 52 N VAL A 44 SHEET 3 B 4 VAL B 51 CYS B 53 -1 O CYS B 53 N VAL A 51 SHEET 4 B 4 VAL B 44 GLN B 45 -1 N VAL B 44 O ILE B 52 SHEET 1 C 2 LYS A 122 VAL A 123 0 SHEET 2 C 2 THR A 140 TYR A 141 1 O THR A 140 N VAL A 123 SHEET 1 D 7 ALA B 56 SER B 57 0 SHEET 2 D 7 LYS B 32 GLY B 37 1 N GLY B 37 O ALA B 56 SHEET 3 D 7 ARG B 5 LEU B 10 1 N LEU B 10 O ALA B 36 SHEET 4 D 7 VAL B 69 LEU B 72 1 O VAL B 71 N LEU B 7 SHEET 5 D 7 LEU B 101 ILE B 105 1 O ALA B 103 N LEU B 72 SHEET 6 D 7 ILE B 152 SER B 155 1 O LEU B 153 N ILE B 102 SHEET 7 D 7 VAL B 146 ASP B 149 -1 N GLU B 147 O THR B 154 SHEET 1 E 2 LYS B 122 VAL B 123 0 SHEET 2 E 2 THR B 140 TYR B 141 1 O THR B 140 N VAL B 123 CISPEP 1 GLY A 65 PRO A 66 0 -0.13 CISPEP 2 GLY B 65 PRO B 66 0 -0.03 CRYST1 75.688 75.688 75.045 90.00 90.00 120.00 P 31 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 0.013212 0.007628 0.000000 0.00000 SCALE2 0.000000 0.015256 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013325 0.00000 MASTER 239 0 0 22 22 0 0 6 0 0 0 30 END