HEADER CHAPERONE 16-OCT-07 2RK4 TITLE STRUCTURE OF M26I DJ-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN DJ-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ONCOGENE DJ1, PARKINSON DISEASE PROTEIN 7; COMPND 5 ENGINEERED: YES; COMPND 6 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 BL21(DE3); 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 PARKINSON'S DISEASE, THIJ, PFPI, CHAPERONE, CYTOPLASM, DISEASE KEYWDS 2 MUTATION, NUCLEUS, ONCOGENE, OXIDATION, PARKINSON DISEASE, KEYWDS 3 PHOSPHORYLATION, POLYMORPHISM, UBL CONJUGATION EXPDTA X-RAY DIFFRACTION AUTHOR M.LAKSHMINARASIMHAN,M.T.MALDONADO,W.ZHOU,A.L.FINK,M.A.WILSON REVDAT 5 30-AUG-23 2RK4 1 REMARK REVDAT 4 20-OCT-21 2RK4 1 SEQADV REVDAT 3 24-FEB-09 2RK4 1 VERSN REVDAT 2 19-FEB-08 2RK4 1 JRNL REVDAT 1 15-JAN-08 2RK4 0 JRNL AUTH M.LAKSHMINARASIMHAN,M.T.MALDONADO,W.ZHOU,A.L.FINK,M.A.WILSON JRNL TITL STRUCTURAL IMPACT OF THREE PARKINSONISM-ASSOCIATED MISSENSE JRNL TITL 2 MUTATIONS ON HUMAN DJ-1. JRNL REF BIOCHEMISTRY V. 47 1381 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18181649 JRNL DOI 10.1021/BI701189C REMARK 2 REMARK 2 RESOLUTION. 1.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.129 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.129 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.156 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 4285 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 85953 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.110 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.136 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 3327 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 67159 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1374 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 255 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1628.5 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1410.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 6 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 15120 REMARK 3 NUMBER OF RESTRAINTS : 18688 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 ANGLE DISTANCES (A) : 0.030 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.030 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.082 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.092 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.029 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.049 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.114 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: BABINET REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2RK4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-OCT-07. REMARK 100 THE DEPOSITION ID IS D_1000044956. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-APR-05 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.827 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL BENT SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 86085 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.56000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHELXL REMARK 200 STARTING MODEL: 1P5F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 3000, 100 MM HEPES, 200 MM REMARK 280 NACL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 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 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 25.02000 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 50.04000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 50.04000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 25.02000 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: 2690 ANGSTROM**2 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -50.04000 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 ASP A 189 REMARK 465 LEU A 190 REMARK 465 GLU A 191 REMARK 465 HIS A 192 REMARK 465 HIS A 193 REMARK 465 HIS A 194 REMARK 465 HIS A 195 REMARK 465 HIS A 196 REMARK 465 HIS A 197 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 LYS A 188 O 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 ARG A 5 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 28 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 LYS A 89 CD - CE - NZ ANGL. DEV. = 16.1 DEGREES REMARK 500 ARG A 145 NE - CZ - NH2 ANGL. DEV. = -3.2 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 CYS A 106 -107.59 72.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2RK3 RELATED DB: PDB REMARK 900 STRUCTURE OF A104T DJ-1 DBREF 2RK4 A 1 189 UNP Q99497 PARK7_HUMAN 1 189 SEQADV 2RK4 ILE A 26 UNP Q99497 MET 26 ENGINEERED MUTATION SEQADV 2RK4 LEU A 190 UNP Q99497 EXPRESSION TAG SEQADV 2RK4 GLU A 191 UNP Q99497 EXPRESSION TAG SEQADV 2RK4 HIS A 192 UNP Q99497 EXPRESSION TAG SEQADV 2RK4 HIS A 193 UNP Q99497 EXPRESSION TAG SEQADV 2RK4 HIS A 194 UNP Q99497 EXPRESSION TAG SEQADV 2RK4 HIS A 195 UNP Q99497 EXPRESSION TAG SEQADV 2RK4 HIS A 196 UNP Q99497 EXPRESSION TAG SEQADV 2RK4 HIS A 197 UNP Q99497 EXPRESSION TAG SEQRES 1 A 197 MET ALA SER LYS ARG ALA LEU VAL ILE LEU ALA LYS GLY SEQRES 2 A 197 ALA GLU GLU MET GLU THR VAL ILE PRO VAL ASP VAL ILE SEQRES 3 A 197 ARG ARG ALA GLY ILE LYS VAL THR VAL ALA GLY LEU ALA SEQRES 4 A 197 GLY LYS ASP PRO VAL GLN CYS SER ARG ASP VAL VAL ILE SEQRES 5 A 197 CYS PRO ASP ALA SER LEU GLU ASP ALA LYS LYS GLU GLY SEQRES 6 A 197 PRO TYR ASP VAL VAL VAL LEU PRO GLY GLY ASN LEU GLY SEQRES 7 A 197 ALA GLN ASN LEU SER GLU SER ALA ALA VAL LYS GLU ILE SEQRES 8 A 197 LEU LYS GLU GLN GLU ASN ARG LYS GLY LEU ILE ALA ALA SEQRES 9 A 197 ILE CYS ALA GLY PRO THR ALA LEU LEU ALA HIS GLU ILE SEQRES 10 A 197 GLY PHE GLY SER LYS VAL THR THR HIS PRO LEU ALA LYS SEQRES 11 A 197 ASP LYS MET MET ASN GLY GLY HIS TYR THR TYR SER GLU SEQRES 12 A 197 ASN ARG VAL GLU LYS ASP GLY LEU ILE LEU THR SER ARG SEQRES 13 A 197 GLY PRO GLY THR SER PHE GLU PHE ALA LEU ALA ILE VAL SEQRES 14 A 197 GLU ALA LEU ASN GLY LYS GLU VAL ALA ALA GLN VAL LYS SEQRES 15 A 197 ALA PRO LEU VAL LEU LYS ASP LEU GLU HIS HIS HIS HIS SEQRES 16 A 197 HIS HIS FORMUL 2 HOH *255(H2 O) HELIX 1 1 GLU A 15 ALA A 29 1 15 HELIX 2 2 LEU A 58 GLU A 64 1 7 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 GLY A 108 HIS A 115 1 8 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 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 ALA A 6 O LYS A 32 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 VAL A 70 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 2 VAL A 44 GLN A 45 0 SHEET 2 B 2 VAL A 51 ILE A 52 -1 O ILE A 52 N VAL A 44 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 CISPEP 1 GLY A 65 PRO A 66 0 4.98 CRYST1 74.770 74.770 75.060 90.00 90.00 120.00 P 31 2 1 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 0.013374 0.007722 0.000000 0.00000 SCALE2 0.000000 0.015443 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013323 0.00000