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 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 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