HEADER BLOOD COAGULATION,OXIDOREDUCTASE 16-NOV-09 3KP9 TITLE STRUCTURE OF A BACTERIAL HOMOLOG OF VITAMIN K EPOXIDE REDUCTASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: VKORC1/THIOREDOXIN DOMAIN PROTEIN; COMPND 3 CHAIN: A; COMPND 4 EC: 1.1.4.2; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCOCCUS SP.; SOURCE 3 ORGANISM_TAXID: 321332; SOURCE 4 STRAIN: JA-2-3B'A(2-13); SOURCE 5 GENE: CYB_2278; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS WARFARIN, DISULFIDE FORMATION, BLOOD COAGULATION, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR W.LI,S.SCHULMAN,R.J.DUTTON,D.BOYD,J.BECKWITH,T.A.RAPOPORT REVDAT 3 13-OCT-21 3KP9 1 REMARK SEQADV REVDAT 2 13-JUL-11 3KP9 1 VERSN REVDAT 1 09-FEB-10 3KP9 0 JRNL AUTH W.LI,S.SCHULMAN,R.J.DUTTON,D.BOYD,J.BECKWITH,T.A.RAPOPORT JRNL TITL STRUCTURE OF A BACTERIAL HOMOLOGUE OF VITAMIN K EPOXIDE JRNL TITL 2 REDUCTASE. JRNL REF NATURE V. 463 507 2010 JRNL REFN ISSN 0028-0836 JRNL PMID 20110994 JRNL DOI 10.1038/NATURE08720 REMARK 2 REMARK 2 RESOLUTION. 3.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 7714 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 + TEST SET) : 0.256 REMARK 3 R VALUE (WORKING SET) : 0.251 REMARK 3 FREE R VALUE : 0.305 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 855 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) : 3.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.70 REMARK 3 REFLECTION IN BIN (WORKING SET) : 558 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.75 REMARK 3 BIN R VALUE (WORKING SET) : 0.2930 REMARK 3 BIN FREE R VALUE SET COUNT : 67 REMARK 3 BIN FREE R VALUE : 0.3740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1963 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.74000 REMARK 3 B22 (A**2) : 2.74000 REMARK 3 B33 (A**2) : -4.12000 REMARK 3 B12 (A**2) : 1.37000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.581 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.333 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 44.419 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.861 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.855 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2051 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2805 ; 1.492 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 256 ; 7.790 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 68 ;38.577 ;22.206 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 299 ;22.001 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;17.564 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 324 ; 0.106 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1519 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1283 ; 0.355 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2056 ; 0.692 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 768 ; 0.847 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 749 ; 1.443 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 16 A 20 REMARK 3 ORIGIN FOR THE GROUP (A): 18.9848 50.9231 12.4686 REMARK 3 T TENSOR REMARK 3 T11: 2.2956 T22: 2.0420 REMARK 3 T33: 1.0831 T12: -1.3821 REMARK 3 T13: 0.5420 T23: 0.5223 REMARK 3 L TENSOR REMARK 3 L11: 46.0780 L22: 15.2841 REMARK 3 L33: 8.2202 L12: 0.5225 REMARK 3 L13: -0.4617 L23: 21.0366 REMARK 3 S TENSOR REMARK 3 S11: 0.0983 S12: -2.9580 S13: 2.3345 REMARK 3 S21: 0.4986 S22: -0.7731 S23: 0.2998 REMARK 3 S31: -0.7482 S32: -1.0585 S33: 0.6748 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 21 A 44 REMARK 3 ORIGIN FOR THE GROUP (A): 40.8754 60.6022 9.7477 REMARK 3 T TENSOR REMARK 3 T11: 0.8842 T22: 1.4523 REMARK 3 T33: 0.7540 T12: -0.3225 REMARK 3 T13: -0.2123 T23: -0.4603 REMARK 3 L TENSOR REMARK 3 L11: -1.7365 L22: 0.7248 REMARK 3 L33: 12.2379 L12: -1.8275 REMARK 3 L13: -1.0054 L23: 2.4627 REMARK 3 S TENSOR REMARK 3 S11: 0.3586 S12: 0.1278 S13: 0.2419 REMARK 3 S21: -0.0183 S22: 0.6247 S23: -0.6276 REMARK 3 S31: 2.1193 S32: 1.0228 S33: -0.9833 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 45 A 70 REMARK 3 ORIGIN FOR THE GROUP (A): 50.9767 73.6483 16.0345 REMARK 3 T TENSOR REMARK 3 T11: 1.4677 T22: 1.0160 REMARK 3 T33: 1.5180 T12: 0.1181 REMARK 3 T13: 0.1213 T23: -0.0426 REMARK 3 L TENSOR REMARK 3 L11: 11.9642 L22: 1.6312 REMARK 3 L33: 2.5931 L12: 6.7598 REMARK 3 L13: -2.2410 L23: -0.1647 REMARK 3 S TENSOR REMARK 3 S11: -0.5028 S12: 1.2689 S13: -0.6467 REMARK 3 S21: -0.6585 S22: 0.4053 S23: -0.4276 REMARK 3 S31: -0.7538 S32: -0.2962 S33: 0.0975 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 71 A 177 REMARK 3 ORIGIN FOR THE GROUP (A): 32.8010 58.6327 22.6571 REMARK 3 T TENSOR REMARK 3 T11: 0.5766 T22: 0.8080 REMARK 3 T33: 0.8180 T12: -0.6024 REMARK 3 T13: -0.1120 T23: 0.1032 REMARK 3 L TENSOR REMARK 3 L11: 7.4344 L22: 2.0072 REMARK 3 L33: 10.6069 L12: 2.4390 REMARK 3 L13: -1.2328 L23: 1.0314 REMARK 3 S TENSOR REMARK 3 S11: 0.1215 S12: 0.2352 S13: -0.4932 REMARK 3 S21: 0.2365 S22: 0.0934 S23: 0.0945 REMARK 3 S31: 1.2643 S32: -1.3395 S33: -0.2149 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 178 A 272 REMARK 3 ORIGIN FOR THE GROUP (A): 58.6703 86.0863 23.6554 REMARK 3 T TENSOR REMARK 3 T11: 0.4952 T22: 0.4649 REMARK 3 T33: 1.1823 T12: -0.0531 REMARK 3 T13: -0.0880 T23: -0.0298 REMARK 3 L TENSOR REMARK 3 L11: 11.3340 L22: 5.3462 REMARK 3 L33: 6.0760 L12: 3.0755 REMARK 3 L13: 3.8060 L23: 0.2514 REMARK 3 S TENSOR REMARK 3 S11: -0.0515 S12: -0.6414 S13: 0.3896 REMARK 3 S21: 0.3344 S22: 0.1206 S23: -0.0264 REMARK 3 S31: -0.3433 S32: -0.2800 S33: -0.0691 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 273 A 279 REMARK 3 ORIGIN FOR THE GROUP (A): 73.3649 85.0948 29.9074 REMARK 3 T TENSOR REMARK 3 T11: 0.6581 T22: 0.6086 REMARK 3 T33: 1.4950 T12: -0.2099 REMARK 3 T13: -0.2752 T23: -0.0166 REMARK 3 L TENSOR REMARK 3 L11: 23.6889 L22: 4.4377 REMARK 3 L33: 16.4774 L12: -10.9828 REMARK 3 L13: 3.9082 L23: 1.5919 REMARK 3 S TENSOR REMARK 3 S11: -1.6816 S12: -0.2654 S13: 1.4188 REMARK 3 S21: 0.7164 S22: 0.0549 S23: -0.3331 REMARK 3 S31: 0.9752 S32: -0.6750 S33: 1.6267 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REMARK 3 REMARK 3 JUDGING FROM THE EXPERIMENTAL ELECTRON DENSITY MAP, THERE IS REMARK 3 DENSITY BETWEEN CYS130 AND CYS133, INDICATIVE OF A DISULFIDE REMARK 3 BRIDGE, AS WELL AS DENSITY SUGGESTING A COVALENT BOND BETWEEN THE REMARK 3 QUINONE RING OF U10 AND CYS133. WE HAVE NOT BEEN ABLE TO USE A REMARK 3 REFINEMENT PROGRAM TO OPTIMIZE BOTH BOND LENGTHS AT THE SAME TIME REMARK 4 REMARK 4 3KP9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000056275. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00718 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8572 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.600 REMARK 200 RESOLUTION RANGE LOW (A) : 118.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MIR REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 78.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG1000, 0.2M MAGNESIUM CHLORIDE, REMARK 280 PH 7, EVAPORATION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 22.82667 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 45.65333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 34.24000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 57.06667 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 11.41333 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 SER A 3 REMARK 465 TYR A 4 REMARK 465 LEU A 5 REMARK 465 LYS A 6 REMARK 465 LEU A 7 REMARK 465 LYS A 8 REMARK 465 ALA A 9 REMARK 465 GLN A 10 REMARK 465 GLU A 11 REMARK 465 GLU A 12 REMARK 465 THR A 13 REMARK 465 TRP A 14 REMARK 465 LEU A 15 REMARK 465 ASP A 53 REMARK 465 GLY A 54 REMARK 465 GLY A 55 REMARK 465 ASP A 91 REMARK 465 GLY A 92 REMARK 465 GLU A 280 REMARK 465 GLU A 281 REMARK 465 GLY A 282 REMARK 465 ARG A 283 REMARK 465 LEU A 284 REMARK 465 GLU A 285 REMARK 465 HIS A 286 REMARK 465 HIS A 287 REMARK 465 HIS A 288 REMARK 465 HIS A 289 REMARK 465 HIS A 290 REMARK 465 HIS A 291 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 LEU A 279 CG CD1 CD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 253 C - N - CD ANGL. DEV. = -13.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 17 -107.23 -124.85 REMARK 500 GLU A 44 136.41 -31.16 REMARK 500 ALA A 48 -60.38 -100.45 REMARK 500 CYS A 50 59.13 -140.49 REMARK 500 THR A 51 154.36 -43.89 REMARK 500 SER A 62 -161.36 -76.20 REMARK 500 TRP A 64 -43.44 81.10 REMARK 500 LEU A 95 -42.92 95.23 REMARK 500 LYS A 97 -68.20 -94.01 REMARK 500 ARG A 152 72.44 44.52 REMARK 500 ASP A 155 77.96 48.90 REMARK 500 PRO A 227 107.23 -56.28 REMARK 500 PRO A 239 132.00 -36.39 REMARK 500 TYR A 252 57.49 -119.26 REMARK 500 ASN A 258 67.81 60.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TYR A 252 PRO A 253 119.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 U10 A 501 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE U10 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 602 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KP8 RELATED DB: PDB REMARK 900 THE THIOREDOXIN-LIKE DOMAIN OF A VKOR HOMOLOG FROM SYNECHOCOCCUS SP. DBREF 3KP9 A 1 283 UNP Q2JJF6 Q2JJF6_SYNJB 1 283 SEQADV 3KP9 SER A 56 UNP Q2JJF6 CYS 56 ENGINEERED MUTATION SEQADV 3KP9 LEU A 284 UNP Q2JJF6 EXPRESSION TAG SEQADV 3KP9 GLU A 285 UNP Q2JJF6 EXPRESSION TAG SEQADV 3KP9 HIS A 286 UNP Q2JJF6 EXPRESSION TAG SEQADV 3KP9 HIS A 287 UNP Q2JJF6 EXPRESSION TAG SEQADV 3KP9 HIS A 288 UNP Q2JJF6 EXPRESSION TAG SEQADV 3KP9 HIS A 289 UNP Q2JJF6 EXPRESSION TAG SEQADV 3KP9 HIS A 290 UNP Q2JJF6 EXPRESSION TAG SEQADV 3KP9 HIS A 291 UNP Q2JJF6 EXPRESSION TAG SEQRES 1 A 291 MET ALA SER TYR LEU LYS LEU LYS ALA GLN GLU GLU THR SEQRES 2 A 291 TRP LEU GLN ARG HIS SER ARG LEU ILE LEU ALA ILE LEU SEQRES 3 A 291 ALA GLY LEU GLY SER LEU LEU THR ALA TYR LEU THR TYR SEQRES 4 A 291 THR LYS LEU THR GLU GLN PRO ALA ALA PHE CYS THR GLY SEQRES 5 A 291 ASP GLY GLY SER ASP LEU VAL LEU SER SER ARG TRP ALA SEQRES 6 A 291 GLU PHE LEU GLY ILE PRO THR ALA ALA VAL GLY LEU LEU SEQRES 7 A 291 GLY PHE LEU GLY VAL LEU ALA LEU ALA VAL LEU PRO ASP SEQRES 8 A 291 GLY LEU PRO LEU VAL LYS ARG TRP ARG TRP PRO ALA LEU SEQRES 9 A 291 PHE GLY LEU VAL SER ALA MET THR ALA PHE GLU MET TYR SEQRES 10 A 291 MET LEU TYR LEU MET VAL ALA VAL LEU ARG GLN PHE CYS SEQRES 11 A 291 MET TYR CYS THR THR ALA ILE ILE LEU VAL ALA GLY LEU SEQRES 12 A 291 GLY LEU VAL THR VAL LEU GLY HIS ARG TRP LEU ASP GLY SEQRES 13 A 291 GLY LYS LEU ALA PHE SER TYR ILE LEU VAL ALA PHE LEU SEQRES 14 A 291 THR LEU VAL THR THR ILE GLY VAL TYR ALA ASN GLN VAL SEQRES 15 A 291 PRO PRO PRO SER PRO LEU ALA VAL GLY LEU ALA ALA HIS SEQRES 16 A 291 LEU ARG GLN ILE GLY GLY THR MET TYR GLY ALA TYR TRP SEQRES 17 A 291 CYS PRO HIS CYS GLN ASP GLN LYS GLU LEU PHE GLY ALA SEQRES 18 A 291 ALA PHE ASP GLN VAL PRO TYR VAL GLU CYS SER PRO ASN SEQRES 19 A 291 GLY PRO GLY THR PRO GLN ALA GLN GLU CYS THR GLU ALA SEQRES 20 A 291 GLY ILE THR SER TYR PRO THR TRP ILE ILE ASN GLY ARG SEQRES 21 A 291 THR TYR THR GLY VAL ARG SER LEU GLU ALA LEU ALA VAL SEQRES 22 A 291 ALA SER GLY TYR PRO LEU GLU GLU GLY ARG LEU GLU HIS SEQRES 23 A 291 HIS HIS HIS HIS HIS HET U10 A 501 33 HET HG A 601 1 HET HG A 602 1 HETNAM U10 UBIQUINONE-10 HETNAM HG MERCURY (II) ION HETSYN U10 COENZYME Q10 FORMUL 2 U10 C59 H90 O4 FORMUL 3 HG 2(HG 2+) HELIX 1 1 ARG A 20 GLU A 44 1 25 HELIX 2 2 LEU A 58 SER A 62 5 5 HELIX 3 3 THR A 72 LEU A 89 1 18 HELIX 4 4 TRP A 99 ALA A 124 1 26 HELIX 5 5 CYS A 130 LEU A 149 1 20 HELIX 6 6 HIS A 151 GLY A 156 1 6 HELIX 7 7 GLY A 157 ASN A 180 1 24 HELIX 8 8 LEU A 188 ILE A 199 1 12 HELIX 9 9 CYS A 209 GLY A 220 1 12 HELIX 10 10 ALA A 221 VAL A 226 5 6 HELIX 11 11 ALA A 241 GLU A 246 1 6 HELIX 12 12 SER A 267 SER A 275 1 9 SHEET 1 A 2 GLU A 66 PHE A 67 0 SHEET 2 A 2 ILE A 70 PRO A 71 -1 O ILE A 70 N PHE A 67 SHEET 1 B 4 TYR A 228 GLU A 230 0 SHEET 2 B 4 THR A 202 GLY A 205 1 N MET A 203 O VAL A 229 SHEET 3 B 4 THR A 254 ILE A 257 -1 O THR A 254 N TYR A 204 SHEET 4 B 4 ARG A 260 THR A 263 -1 O TYR A 262 N TRP A 255 SSBOND 1 CYS A 50 CYS A 209 1555 1555 2.04 SSBOND 2 CYS A 130 CYS A 133 1555 1555 2.06 SSBOND 3 CYS A 231 CYS A 244 1555 1555 2.04 LINK ND1 HIS A 195 HG HG A 602 1555 1555 2.01 LINK SG CYS A 212 HG HG A 601 1555 1555 1.76 SITE 1 AC1 14 VAL A 59 ARG A 63 TRP A 64 ALA A 65 SITE 2 AC1 14 THR A 72 ALA A 73 VAL A 75 GLY A 76 SITE 3 AC1 14 MET A 111 PHE A 114 MET A 118 LEU A 126 SITE 4 AC1 14 CYS A 133 THR A 170 SITE 1 AC2 2 CYS A 212 TYR A 228 SITE 1 AC3 1 HIS A 195 CRYST1 136.942 136.942 68.480 90.00 90.00 120.00 P 61 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 0.007302 0.004216 0.000000 0.00000 SCALE2 0.000000 0.008432 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014603 0.00000