PDB Short entry for 1P5F HEADER UNKNOWN FUNCTION 26-APR-03 1P5F TITLE CRYSTAL STRUCTURE OF HUMAN DJ-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA-BINDING PROTEIN REGULATORY SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-15B KEYWDS UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR M.A.WILSON,J.L.COLLINS,Y.HOD,D.RINGE,G.A.PETSKO REVDAT 6 14-FEB-24 1P5F 1 REMARK REVDAT 5 31-JAN-18 1P5F 1 REMARK REVDAT 4 11-OCT-17 1P5F 1 REMARK REVDAT 3 13-JUL-11 1P5F 1 VERSN REVDAT 2 24-FEB-09 1P5F 1 VERSN REVDAT 1 12-AUG-03 1P5F 0 JRNL AUTH M.A.WILSON,J.L.COLLINS,Y.HOD,D.RINGE,G.A.PETSKO JRNL TITL THE 1.1 A RESOLUTION CRYSTAL STRUCTURE OF DJ-1, THE PROTEIN JRNL TITL 2 MUTATED IN AUTOSOMAL RECESSIVE EARLY ONSET PARKINSON'S JRNL TITL 3 DISEASE JRNL REF PROC.NATL.ACAD.SCI.USA V. 100 9256 2003 JRNL REFN ISSN 0027-8424 JRNL PMID 12855764 JRNL DOI 10.1073/PNAS.1133288100 REMARK 2 REMARK 2 RESOLUTION. 1.10 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) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 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) : 0.139 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.139 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.161 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 4714 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 99689 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.129 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.129 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.155 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 3998 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 78833 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1370 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 252 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1551.6 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1392.6 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 18 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 15913 REMARK 3 NUMBER OF RESTRAINTS : 21047 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 ANGLE DISTANCES (A) : 0.032 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.031 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.084 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.100 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.075 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.047 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.103 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1P5F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-APR-03. REMARK 100 THE DEPOSITION ID IS D_1000019029. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-AUG-02 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 : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : BENT GE(111) REMARK 200 OPTICS : CONICAL SI MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 99689 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 33.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 36.4000 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) : 1.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.54200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: SOLVE, RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 400, TRIS-HCL, SODIUM CITRATE, PH REMARK 280 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 23K, TEMPERATURE REMARK 280 296.0K 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 25.14067 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 50.28133 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 50.28133 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 25.14067 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 REMARK: THE BIOLOGICAL ASSEMBLY IS A DIMER GENERATED FROM THE REMARK 300 MONOMER IN THE ASYMMETRIC UNIT BY THE OPERATIONS: Y, X, -Z+1 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: 2680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 -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 75.42200 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 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 398 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 ALA A 2 REMARK 465 ASP A 189 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 SER A 3 N - CA - CB ANGL. DEV. = 9.9 DEGREES REMARK 500 SER A 3 CA - C - O ANGL. DEV. = -21.5 DEGREES REMARK 500 SER A 3 CA - C - N ANGL. DEV. = 16.7 DEGREES REMARK 500 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 GLU A 96 OE1 - CD - OE2 ANGL. DEV. = -7.4 DEGREES REMARK 500 ARG A 98 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 CYS A 106 CA - C - N ANGL. DEV. = 13.6 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 -101.02 77.01 REMARK 500 REMARK 500 REMARK: NULL DBREF 1P5F A 1 189 UNP Q99497 PARK7_HUMAN 1 189 SEQRES 1 A 189 MET ALA SER LYS ARG ALA LEU VAL ILE LEU ALA LYS GLY SEQRES 2 A 189 ALA GLU GLU MET GLU THR VAL ILE PRO VAL ASP VAL MET SEQRES 3 A 189 ARG ARG ALA GLY ILE LYS VAL THR VAL ALA GLY LEU ALA SEQRES 4 A 189 GLY LYS ASP PRO VAL GLN CYS SER ARG ASP VAL VAL ILE SEQRES 5 A 189 CYS PRO ASP ALA SER LEU GLU ASP ALA LYS LYS GLU GLY SEQRES 6 A 189 PRO TYR ASP VAL VAL VAL LEU PRO GLY GLY ASN LEU GLY SEQRES 7 A 189 ALA GLN ASN LEU SER GLU SER ALA ALA VAL LYS GLU ILE SEQRES 8 A 189 LEU LYS GLU GLN GLU ASN ARG LYS GLY LEU ILE ALA ALA SEQRES 9 A 189 ILE CYS ALA GLY PRO THR ALA LEU LEU ALA HIS GLU ILE SEQRES 10 A 189 GLY PHE GLY SER LYS VAL THR THR HIS PRO LEU ALA LYS SEQRES 11 A 189 ASP LYS MET MET ASN GLY GLY HIS TYR THR TYR SER GLU SEQRES 12 A 189 ASN ARG VAL GLU LYS ASP GLY LEU ILE LEU THR SER ARG SEQRES 13 A 189 GLY PRO GLY THR SER PHE GLU PHE ALA LEU ALA ILE VAL SEQRES 14 A 189 GLU ALA LEU ASN GLY LYS GLU VAL ALA ALA GLN VAL LYS SEQRES 15 A 189 ALA PRO LEU VAL LEU LYS ASP FORMUL 2 HOH *252(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 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 VAL A 70 SHEET 6 A 7 ILE A 152 SER A 155 1 O LEU A 153 N ALA A 104 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 6.06 CRYST1 75.306 75.306 75.422 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 0.013279 0.007667 0.000000 0.00000 SCALE2 0.000000 0.015333 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013259 0.00000