HEADER HYDROLASE 26-JUN-24 9CEI TITLE HUMAN DJ-1, NO MIXING, PINK BEAM TIME-RESOLVED SERIAL CRYSTALLOGRAPHY COMPND MOL_ID: 1; COMPND 2 MOLECULE: PARKINSON DISEASE PROTEIN 7; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MAILLARD DEGLYCASE,ONCOGENE DJ1,PARKINSONISM-ASSOCIATED COMPND 5 DEGLYCASE,PROTEIN DJ-1,DJ-1,PROTEIN/NUCLEIC ACID DEGLYCASE DJ-1; COMPND 6 EC: 3.1.2.-,3.5.1.-,3.5.1.124; COMPND 7 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS GLUTATHIONE-INDEPENDENT GLYOXALASE, SERIAL CRYSTALLOGRAPHY, LAUE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.A.ZIELINSKI,C.DOLAMORE,K.DALTON,S.P.MEISBURGER,N.SMITH,J.TERMINI, AUTHOR 2 R.HENNING,V.SRAJER,D.HEKSTRA,L.POLLACK,M.A.WILSON REVDAT 2 02-SEP-26 9CEI 1 CAVEAT REMARK LINK ATOM REVDAT 1 12-MAR-25 9CEI 0 JRNL AUTH K.A.ZIELINSKI,C.DOLAMORE,K.M.DALTON,N.SMITH,J.TERMINI, JRNL AUTH 2 R.HENNING,V.SRAJER,D.R.HEKSTRA,L.POLLACK,M.A.WILSON JRNL TITL RESOLVING DJ-1 GLYOXALASE CATALYSIS USING MIX-AND-INJECT JRNL TITL 2 SERIAL CRYSTALLOGRAPHY AT A SYNCHROTRON. JRNL REF BIORXIV 2024 JRNL REFN ISSN 2692-8205 JRNL PMID 39071394 JRNL DOI 10.1101/2024.07.19.604369 REMARK 2 REMARK 2 RESOLUTION. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 65.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.750 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 25191 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.550 REMARK 3 FREE R VALUE TEST SET COUNT : 1145 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 65.8400 - 3.5400 0.99 3157 132 0.1395 0.1684 REMARK 3 2 3.5400 - 2.8100 1.00 3021 153 0.1461 0.1592 REMARK 3 3 2.8100 - 2.4500 1.00 2994 137 0.1558 0.1992 REMARK 3 4 2.4500 - 2.2300 1.00 3036 129 0.1658 0.2203 REMARK 3 5 2.2300 - 2.0700 1.00 2976 149 0.2159 0.2112 REMARK 3 6 2.0700 - 1.9500 1.00 2949 157 0.2493 0.2869 REMARK 3 7 1.9500 - 1.8500 1.00 2969 133 0.3056 0.3528 REMARK 3 8 1.8500 - 1.7700 1.00 2944 155 0.3265 0.3276 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.266 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : -0.52 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 1470 REMARK 3 ANGLE : 0.646 1996 REMARK 3 CHIRALITY : 0.045 234 REMARK 3 PLANARITY : 0.005 264 REMARK 3 DIHEDRAL : 15.188 574 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9CEI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JUL-24. REMARK 100 THE DEPOSITION ID IS D_1000285354. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-22 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : L REMARK 200 WAVELENGTH OR RANGE (A) : 1.240-1.016 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX340-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PRECOGNITION REMARK 200 DATA SCALING SOFTWARE : CARELESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25220 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 65.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 65.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 21.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.220 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: LAUE REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES PH=7.5, 200 MM NACL, AND REMARK 280 15% PEG 3350, PH 7.5, BATCH MODE, TEMPERATURE 293K 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 25.38000 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 50.76000 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 50.76000 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 25.38000 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: 2820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15140 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 50.76000 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 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 CSO A 106 -109.81 72.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9CFI RELATED DB: PDB REMARK 900 RELATED ID: 9CFM RELATED DB: PDB REMARK 900 RELATED ID: 9CFO RELATED DB: PDB REMARK 900 RELATED ID: 9CFY RELATED DB: PDB REMARK 900 RELATED ID: 9CFZ RELATED DB: PDB REMARK 900 RELATED ID: 9CG0 RELATED DB: PDB DBREF 9CEI A 1 189 UNP Q99497 PARK7_HUMAN 1 189 SEQADV 9CEI GLY A -2 UNP Q99497 EXPRESSION TAG SEQADV 9CEI SER A -1 UNP Q99497 EXPRESSION TAG SEQADV 9CEI HIS A 0 UNP Q99497 EXPRESSION TAG SEQRES 1 A 192 GLY SER HIS MET ALA SER LYS ARG ALA LEU VAL ILE LEU SEQRES 2 A 192 ALA LYS GLY ALA GLU GLU MET GLU THR VAL ILE PRO VAL SEQRES 3 A 192 ASP VAL MET ARG ARG ALA GLY ILE LYS VAL THR VAL ALA SEQRES 4 A 192 GLY LEU ALA GLY LYS ASP PRO VAL GLN CYS SER ARG ASP SEQRES 5 A 192 VAL VAL ILE CYS PRO ASP ALA SER LEU GLU ASP ALA LYS SEQRES 6 A 192 LYS GLU GLY PRO TYR ASP VAL VAL VAL LEU PRO GLY GLY SEQRES 7 A 192 ASN LEU GLY ALA GLN ASN LEU SER GLU SER ALA ALA VAL SEQRES 8 A 192 LYS GLU ILE LEU LYS GLU GLN GLU ASN ARG LYS GLY LEU SEQRES 9 A 192 ILE ALA ALA ILE CSO ALA GLY PRO THR ALA LEU LEU ALA SEQRES 10 A 192 HIS GLU ILE GLY PHE GLY SER LYS VAL THR THR HIS PRO SEQRES 11 A 192 LEU ALA LYS ASP LYS MET MET ASN GLY GLY HIS TYR THR SEQRES 12 A 192 TYR SER GLU ASN ARG VAL GLU LYS ASP GLY LEU ILE LEU SEQRES 13 A 192 THR SER ARG GLY PRO GLY THR SER PHE GLU PHE ALA LEU SEQRES 14 A 192 ALA ILE VAL GLU ALA LEU ASN GLY LYS GLU VAL ALA ALA SEQRES 15 A 192 GLN VAL LYS ALA PRO LEU VAL LEU LYS ASP MODRES 9CEI CSO A 106 CYS MODIFIED RESIDUE HET CSO A 106 11 HETNAM CSO S-HYDROXYCYSTEINE FORMUL 1 CSO C3 H7 N O3 S FORMUL 2 HOH *136(H2 O) HELIX 1 AA1 GLU A 15 ALA A 29 1 15 HELIX 2 AA2 LEU A 58 GLU A 64 1 7 HELIX 3 AA3 GLY A 75 GLU A 84 1 10 HELIX 4 AA4 SER A 85 ARG A 98 1 14 HELIX 5 AA5 PRO A 109 HIS A 115 1 7 HELIX 6 AA6 HIS A 126 LEU A 128 5 3 HELIX 7 AA7 ALA A 129 MET A 134 1 6 HELIX 8 AA8 GLY A 157 GLY A 159 5 3 HELIX 9 AA9 THR A 160 GLY A 174 1 15 HELIX 10 AB1 GLY A 174 ALA A 183 1 10 HELIX 11 AB2 PRO A 184 VAL A 186 5 3 SHEET 1 AA1 7 ALA A 56 SER A 57 0 SHEET 2 AA1 7 LYS A 32 GLY A 37 1 N GLY A 37 O ALA A 56 SHEET 3 AA1 7 ARG A 5 LEU A 10 1 N VAL A 8 O ALA A 36 SHEET 4 AA1 7 VAL A 69 LEU A 72 1 O VAL A 71 N LEU A 7 SHEET 5 AA1 7 LEU A 101 ILE A 105 1 O ALA A 103 N VAL A 70 SHEET 6 AA1 7 ILE A 152 SER A 155 1 O LEU A 153 N ILE A 102 SHEET 7 AA1 7 VAL A 146 ASP A 149 -1 N GLU A 147 O THR A 154 SHEET 1 AA2 2 VAL A 44 GLN A 45 0 SHEET 2 AA2 2 VAL A 51 ILE A 52 -1 O ILE A 52 N VAL A 44 SHEET 1 AA3 2 LYS A 122 VAL A 123 0 SHEET 2 AA3 2 THR A 140 TYR A 141 1 O THR A 140 N VAL A 123 LINK C ILE A 105 N CSO A 106 1555 1555 1.33 LINK C CSO A 106 N ALA A 107 1555 1555 1.33 CISPEP 1 GLY A 65 PRO A 66 0 -2.25 CRYST1 76.030 76.030 76.140 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 0.013153 0.007594 0.000000 0.00000 SCALE2 0.000000 0.015187 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013134 0.00000 CONECT 1623 1640 CONECT 1640 1623 1641 CONECT 1641 1640 1642 1644 1647 CONECT 1642 1641 1643 1648 1649 CONECT 1643 1642 1646 CONECT 1644 1641 1645 1651 CONECT 1645 1644 CONECT 1646 1643 1650 CONECT 1647 1641 CONECT 1648 1642 CONECT 1649 1642 CONECT 1650 1646 CONECT 1651 1644 MASTER 247 0 1 11 11 0 0 6 1521 1 13 15 END