HEADER RNA BINDING PROTEIN 26-FEB-03 1J42
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 SYNONYM: DJ-1;
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 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET21A
KEYWDS PARKINSON'S DISEASE, RNA BINDING PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR S.S.CHA
REVDAT 5 27-DEC-23 1J42 1 REMARK
REVDAT 4 04-OCT-17 1J42 1 REMARK
REVDAT 3 13-JUL-11 1J42 1 VERSN
REVDAT 2 24-FEB-09 1J42 1 VERSN
REVDAT 1 03-FEB-04 1J42 0
JRNL AUTH S.J.LEE,S.J.KIM,I.K.KIM,J.KO,C.S.JEONG,G.H.KIM,C.PARK,
JRNL AUTH 2 S.O.KANG,P.G.SUH,H.S.LEE,S.S.CHA
JRNL TITL CRYSTAL STRUCTURES OF HUMAN DJ-1 AND ESCHERICHIA COLI HSP31,
JRNL TITL 2 WHICH SHARE AN EVOLUTIONARILY CONSERVED DOMAIN.
JRNL REF J.BIOL.CHEM. V. 278 44552 2003
JRNL REFN ISSN 0021-9258
JRNL PMID 12939276
JRNL DOI 10.1074/JBC.M304517200
REMARK 2
REMARK 2 RESOLUTION. 2.50 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.1
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) : 2.50
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.84
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 298114.110
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.5
REMARK 3 NUMBER OF REFLECTIONS : 8683
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 SET) : 0.228
REMARK 3 FREE R VALUE : 0.249
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.700
REMARK 3 FREE R VALUE TEST SET COUNT : 930
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 6
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.30
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1231
REMARK 3 BIN R VALUE (WORKING SET) : 0.2680
REMARK 3 BIN FREE R VALUE : 0.2630
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.60
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 130
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1330
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 41
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 31.60
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.90
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 2.81000
REMARK 3 B22 (A**2) : 4.36000
REMARK 3 B33 (A**2) : -7.17000
REMARK 3 B12 (A**2) : 4.48000
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) : 0.31
REMARK 3 ESD FROM SIGMAA (A) : 0.30
REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.35
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.29
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.010
REMARK 3 BOND ANGLES (DEGREES) : 1.400
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.10
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.000
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : 0.000 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 0.000 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 0.000 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 0.000 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.38
REMARK 3 BSOL : 39.48
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 : WATER_REP.PARAM
REMARK 3 PARAMETER FILE 3 : NULL
REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
REMARK 3 TOPOLOGY FILE 2 : NULL
REMARK 3 TOPOLOGY FILE 3 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1J42 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-FEB-03.
REMARK 100 THE DEPOSITION ID IS D_1000005604.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 10-OCT-02
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : OSMIC MIRROR
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8696
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
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 (%): 61.08
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.19
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE, EVAPORATION,
REMARK 280 TEMPERATURE 295K, PH 4-9, PH 6.5
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 25.05267
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 50.10533
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 50.10533
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 25.05267
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 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: MONOMERIC
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
REMARK 350 BIOMOLECULE: 2
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA,PQS
REMARK 350 TOTAL BURIED SURFACE AREA: 2510 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 14310 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 225.22500
REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 -130.03371
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -75.15800
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 LYS A 188
REMARK 465 ASP A 189
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 41 CG CD CE NZ
REMARK 470 GLU A 59 CG CD OE1 OE2
REMARK 470 GLU A 90 CG CD OE1 OE2
REMARK 470 GLU A 94 CG CD OE1 OE2
REMARK 470 ARG A 98 CG CD NE CZ NH1 NH2
REMARK 470 GLU A 176 CG CD OE1 OE2
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 -113.37 64.52
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1J42 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 CYS 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 *41(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 GLU A 84 1 10
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 ASN A 135 1 7
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 69 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 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
CRYST1 75.075 75.075 75.158 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 0.013320 0.007690 0.000000 0.00000
SCALE2 0.000000 0.015381 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013305 0.00000
(ATOM LINES ARE NOT SHOWN.)
END