HEADER OXIDOREDUCTASE 22-SEP-09 3JYL TITLE CRYSTAL STRUCTURES OF PSEUDOMONAS SYRINGAE PV. TOMATO DC3000 QUINONE TITLE 2 OXIDOREDUCTASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: QUINONE OXIDOREDUCTASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.6.5.5; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS SYRINGAE PV. TOMATO; SOURCE 3 ORGANISM_TAXID: 323; SOURCE 4 STRAIN: DC3000; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; 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: PGEX-6P-1 KEYWDS ROSSMANN FOLD, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR X.PAN,H.ZHANG,Y.GAO,M.LI,W.CHANG REVDAT 2 01-NOV-23 3JYL 1 REMARK REVDAT 1 12-JAN-10 3JYL 0 JRNL AUTH X.PAN,H.ZHANG,Y.GAO,M.LI,W.CHANG JRNL TITL CRYSTAL STRUCTURES OF PSEUDOMONAS SYRINGAE PV. TOMATO DC3000 JRNL TITL 2 QUINONE OXIDOREDUCTASE AND ITS COMPLEX WITH NADPH JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 390 597 2009 JRNL REFN ISSN 0006-291X JRNL PMID 19818736 JRNL DOI 10.1016/J.BBRC.2009.10.012 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.24 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) (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 11793 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) : 0.202 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 636 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 : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 818 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE : 0.3110 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 57 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 : 2422 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 253 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.76000 REMARK 3 B22 (A**2) : -0.76000 REMARK 3 B33 (A**2) : 1.14000 REMARK 3 B12 (A**2) : -0.38000 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) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.330 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : MASK REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3JYL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1000055322. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12429 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 23.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.53000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1QOR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL(PH 8.5), 0.2M MGCL2, REMARK 280 30%PEG4000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K, PH REMARK 280 7.5 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 43.38300 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 86.76600 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 86.76600 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 43.38300 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: 2140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 43.38300 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 LEU A 121 -34.95 -155.37 REMARK 500 MET A 122 -74.01 -52.50 REMARK 500 LYS A 209 -168.47 61.57 REMARK 500 ASP A 257 51.13 78.30 REMARK 500 ALA A 273 26.10 -73.27 REMARK 500 GLN A 274 -33.23 -148.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3JYN RELATED DB: PDB DBREF 3JYL A 1 325 UNP Q88B47 Q88B47_PSESM 1 325 SEQRES 1 A 325 MET ALA LYS ARG ILE GLN PHE SER THR VAL GLY GLY PRO SEQRES 2 A 325 GLU VAL LEU GLU TYR VAL ASP PHE GLU PRO GLU ALA PRO SEQRES 3 A 325 GLY PRO GLN ALA VAL VAL VAL ARG ASN LYS ALA ILE GLY SEQRES 4 A 325 LEU ASN PHE ILE ASP THR TYR TYR ARG SER GLY LEU TYR SEQRES 5 A 325 PRO ALA PRO PHE LEU PRO SER GLY LEU GLY ALA GLU GLY SEQRES 6 A 325 ALA GLY VAL VAL GLU ALA VAL GLY ASP GLU VAL THR ARG SEQRES 7 A 325 PHE LYS VAL GLY ASP ARG VAL ALA TYR GLY THR GLY PRO SEQRES 8 A 325 LEU GLY ALA TYR SER GLU VAL HIS VAL LEU PRO GLU ALA SEQRES 9 A 325 ASN LEU VAL LYS LEU ALA ASP SER VAL SER PHE GLU GLN SEQRES 10 A 325 ALA ALA ALA LEU MET LEU LYS GLY LEU THR VAL GLN TYR SEQRES 11 A 325 LEU LEU ARG GLN THR TYR GLN VAL LYS PRO GLY GLU ILE SEQRES 12 A 325 ILE LEU PHE HIS ALA ALA ALA GLY GLY VAL GLY SER LEU SEQRES 13 A 325 ALA CYS GLN TRP ALA LYS ALA LEU GLY ALA LYS LEU ILE SEQRES 14 A 325 GLY THR VAL SER SER PRO GLU LYS ALA ALA HIS ALA LYS SEQRES 15 A 325 ALA LEU GLY ALA TRP GLU THR ILE ASP TYR SER HIS GLU SEQRES 16 A 325 ASP VAL ALA LYS ARG VAL LEU GLU LEU THR ASP GLY LYS SEQRES 17 A 325 LYS CYS PRO VAL VAL TYR ASP GLY VAL GLY GLN ASP THR SEQRES 18 A 325 TRP LEU THR SER LEU ASP SER VAL ALA PRO ARG GLY LEU SEQRES 19 A 325 VAL VAL SER PHE GLY ASN ALA SER GLY PRO VAL SER GLY SEQRES 20 A 325 VAL ASN LEU GLY ILE LEU ALA GLN LYS ASP SER VAL TYR SEQRES 21 A 325 VAL THR ARG PRO THR LEU GLY SER TYR ALA ASN ASN ALA SEQRES 22 A 325 GLN ASN LEU GLN THR MET ALA ASP GLU LEU PHE ASP MET SEQRES 23 A 325 LEU ALA SER GLY LYS LEU LYS VAL ASP GLY ILE GLU GLN SEQRES 24 A 325 TYR ALA LEU LYS ASP ALA ALA LYS ALA GLN ILE GLU LEU SEQRES 25 A 325 SER ALA ARG ARG THR THR GLY SER THR ILE LEU ILE PRO FORMUL 2 HOH *253(H2 O) HELIX 1 1 GLY A 12 LEU A 16 5 5 HELIX 2 2 ASN A 41 SER A 49 1 9 HELIX 3 3 ALA A 104 LEU A 106 5 3 HELIX 4 4 SER A 114 ALA A 120 1 7 HELIX 5 5 LEU A 121 GLN A 134 1 14 HELIX 6 6 GLY A 151 GLY A 165 1 15 HELIX 7 7 SER A 174 GLY A 185 1 12 HELIX 8 8 ASP A 196 THR A 205 1 10 HELIX 9 9 GLY A 218 ASP A 220 5 3 HELIX 10 10 THR A 221 SER A 228 1 8 HELIX 11 11 LEU A 250 LYS A 256 1 7 HELIX 12 12 THR A 265 ALA A 270 1 6 HELIX 13 13 GLN A 274 SER A 289 1 16 HELIX 14 14 ASP A 304 ARG A 315 1 12 SHEET 1 A 2 ALA A 2 GLN A 6 0 SHEET 2 A 2 GLU A 17 PHE A 21 -1 O VAL A 19 N ARG A 4 SHEET 1 B 5 VAL A 98 PRO A 102 0 SHEET 2 B 5 ALA A 30 GLY A 39 -1 N VAL A 33 O HIS A 99 SHEET 3 B 5 GLY A 65 VAL A 72 -1 O GLU A 70 N VAL A 32 SHEET 4 B 5 ARG A 84 TYR A 87 -1 O VAL A 85 N GLY A 67 SHEET 5 B 5 VAL A 107 LYS A 108 -1 O VAL A 107 N ALA A 86 SHEET 1 C 4 VAL A 98 PRO A 102 0 SHEET 2 C 4 ALA A 30 GLY A 39 -1 N VAL A 33 O HIS A 99 SHEET 3 C 4 SER A 320 ILE A 324 -1 O LEU A 323 N ILE A 38 SHEET 4 C 4 ILE A 297 ALA A 301 1 N GLU A 298 O SER A 320 SHEET 1 D 6 GLU A 188 ASP A 191 0 SHEET 2 D 6 LYS A 167 VAL A 172 1 N GLY A 170 O ILE A 190 SHEET 3 D 6 ILE A 143 PHE A 146 1 N ILE A 144 O ILE A 169 SHEET 4 D 6 CYS A 210 ASP A 215 1 O TYR A 214 N LEU A 145 SHEET 5 D 6 VAL A 229 SER A 237 1 O VAL A 236 N ASP A 215 SHEET 6 D 6 TYR A 260 THR A 262 1 O TYR A 260 N GLY A 233 CISPEP 1 LEU A 57 PRO A 58 0 -0.94 CRYST1 63.560 63.560 130.149 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 0.015733 0.009084 0.000000 0.00000 SCALE2 0.000000 0.018167 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007684 0.00000