HEADER LYASE 16-JAN-14 4OGF
TITLE CRYSTAL STRUCTURE OF HUMAN DJ-1 WITH GLYOXYLATE AS SUBSTRATE ANALOG
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 EC: 4.2.1.130;
COMPND 6 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
KEYWDS GLYOXALASE, LYASE
EXPDTA X-RAY DIFFRACTION
AUTHOR D.CHOI,J.KIM,K.-S.RYU,C.PARK
REVDAT 4 20-SEP-23 4OGF 1 LINK
REVDAT 3 24-DEC-14 4OGF 1 JRNL
REVDAT 2 22-OCT-14 4OGF 1 JRNL
REVDAT 1 15-OCT-14 4OGF 0
JRNL AUTH D.CHOI,J.KIM,S.HA,K.KWON,E.H.KIM,H.Y.LEE,K.S.RYU,C.PARK
JRNL TITL STEREOSPECIFIC MECHANISM OF DJ-1 GLYOXALASES INFERRED FROM
JRNL TITL 2 THEIR HEMITHIOACETAL-CONTAINING CRYSTAL STRUCTURES.
JRNL REF FEBS J. V. 281 5447 2014
JRNL REFN ISSN 1742-464X
JRNL PMID 25283443
JRNL DOI 10.1111/FEBS.13085
REMARK 2
REMARK 2 RESOLUTION. 1.60 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) : 1.60
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00
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) (%) : 99.1
REMARK 3 NUMBER OF REFLECTIONS : 32064
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) : 0.212
REMARK 3 FREE R VALUE : 0.235
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.700
REMARK 3 FREE R VALUE TEST SET COUNT : 3205
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 : 10
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.58
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.66
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 68.60
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2917
REMARK 3 BIN R VALUE (WORKING SET) : 0.3987
REMARK 3 BIN FREE R VALUE : 0.3912
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 341
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 : 1381
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 127
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.15
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 2.85400
REMARK 3 B22 (A**2) : 2.85400
REMARK 3 B33 (A**2) : -5.70800
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 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) : NULL
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) : 1.142 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.733 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 2.246 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.239 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : NULL
REMARK 3 KSOL : NULL
REMARK 3 BSOL : 43.49
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 : CNS_TOPPAR:PROTEIN_REP.PARAM
REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:DNA-RNA_REP.PARAM
REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:WATER_REP.PARAM
REMARK 3 PARAMETER FILE 4 : CNS_TOPPAR:ION.PARAM
REMARK 3 PARAMETER FILE 5 : CNS_TOPPAR:CARBOHYDRATE.PARAM
REMARK 3 PARAMETER FILE 6 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3 TOPOLOGY FILE 2 : NULL
REMARK 3 TOPOLOGY FILE 3 : NULL
REMARK 3 TOPOLOGY FILE 4 : NULL
REMARK 3 TOPOLOGY FILE 5 : NULL
REMARK 3 TOPOLOGY FILE 6 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 4OGF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JAN-14.
REMARK 100 THE DEPOSITION ID IS D_1000084460.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 29-MAY-12
REMARK 200 TEMPERATURE (KELVIN) : NULL
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : PHOTON FACTORY
REMARK 200 BEAMLINE : BL-17A
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 : DOUBLE CRYSTAL SI(111)
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32086
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1
REMARK 200 DATA REDUNDANCY : 7.400
REMARK 200 R MERGE (I) : 0.04700
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66
REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4
REMARK 200 DATA REDUNDANCY IN SHELL : 4.40
REMARK 200 R MERGE FOR SHELL (I) : 0.39200
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: COOT
REMARK 200 STARTING MODEL: PDB ENTRY 1PDV
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 59.75
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, 1.4 M SODIUM CITRATE, PH
REMARK 280 7.5, VAPOR DIFFUSION, HANGING DROP
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 24.97900
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 49.95800
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 49.95800
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 24.97900
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: 2670 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 14830 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 -49.95800
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 CGV A 106 -101.48 63.64
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4OFW RELATED DB: PDB
REMARK 900 RELATED ID: 4OGG RELATED DB: PDB
DBREF 4OGF A 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 CGV 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
MODRES 4OGF CGV A 106 CYS
HET CGV A 106 11
HETNAM CGV S-[(R)-CARBOXY(HYDROXY)METHYL]-L-CYSTEINE
FORMUL 1 CGV C5 H9 N O5 S
FORMUL 2 HOH *127(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
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 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
SSBOND 1 CYS A 53 CYS A 53 1555 6554 2.93
LINK C ILE A 105 N CGV A 106 1555 1555 1.33
LINK C CGV A 106 N ALA A 107 1555 1555 1.33
CISPEP 1 GLY A 65 PRO A 66 0 -0.03
CRYST1 74.692 74.692 74.937 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 0.013388 0.007730 0.000000 0.00000
SCALE2 0.000000 0.015459 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013345 0.00000
(ATOM LINES ARE NOT SHOWN.)
END