HEADER OXIDOREDUCTASE 04-DEC-13 4NV5 TITLE C50A MUTANT OF SYNECHOCOCCUS VKOR, C2 CRYSTAL FORM (DEHYDRATED) COMPND MOL_ID: 1; COMPND 2 MOLECULE: VKORC1/THIOREDOXIN DOMAIN PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 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: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET20B KEYWDS FOUR HELIX BUNDLE, OXIDOREDUCTASE, THIOREDOXIN-LIKE PROTEIN, MEMBRANE EXPDTA X-RAY DIFFRACTION AUTHOR S.LIU,W.CHENG,R.FOWLE GRIDER,G.SHEN,W.LI REVDAT 2 09-OCT-24 4NV5 1 REMARK SEQADV REVDAT 1 12-FEB-14 4NV5 0 JRNL AUTH S.LIU,W.CHENG,R.FOWLE GRIDER,G.SHEN,W.LI JRNL TITL STRUCTURES OF AN INTRAMEMBRANE VITAMIN K EPOXIDE REDUCTASE JRNL TITL 2 HOMOLOG REVEAL CONTROL MECHANISMS FOR ELECTRON TRANSFER. JRNL REF NAT COMMUN V. 5 3110 2014 JRNL REFN ESSN 2041-1723 JRNL PMID 24477003 JRNL DOI 10.1038/NCOMMS4110 REMARK 2 REMARK 2 RESOLUTION. 2.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 2.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 24812 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) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2733 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) : 2.79 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1678 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.10 REMARK 3 BIN R VALUE (WORKING SET) : 0.2940 REMARK 3 BIN FREE R VALUE SET COUNT : 198 REMARK 3 BIN FREE R VALUE : 0.3340 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3929 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 77.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -49.48000 REMARK 3 B22 (A**2) : 18.91000 REMARK 3 B33 (A**2) : 30.57000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.25000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.094 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.059 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.188 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.712 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.915 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.899 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4105 ; 0.005 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5616 ; 0.900 ; 1.991 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 515 ; 4.071 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 135 ;33.900 ;22.444 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 595 ;15.443 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;13.868 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 648 ; 0.053 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3061 ; 0.004 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 2 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.664 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : H,-K,-L REMARK 3 TWIN FRACTION : 0.336 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 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 17 A 282 REMARK 3 ORIGIN FOR THE GROUP (A): -22.4626 20.6596 -19.3963 REMARK 3 T TENSOR REMARK 3 T11: 0.4819 T22: 0.3643 REMARK 3 T33: 0.0138 T12: -0.0726 REMARK 3 T13: 0.0356 T23: 0.0305 REMARK 3 L TENSOR REMARK 3 L11: 5.0593 L22: 2.0289 REMARK 3 L33: 0.5214 L12: 2.2200 REMARK 3 L13: -0.7126 L23: -0.0241 REMARK 3 S TENSOR REMARK 3 S11: -0.0270 S12: -0.0584 S13: -0.1958 REMARK 3 S21: 0.0141 S22: -0.0080 S23: -0.0576 REMARK 3 S31: 0.1529 S32: -0.1138 S33: 0.0350 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 : B 13 B 279 REMARK 3 ORIGIN FOR THE GROUP (A): -50.2161 6.6868 14.6427 REMARK 3 T TENSOR REMARK 3 T11: 0.5274 T22: 0.4177 REMARK 3 T33: 0.0588 T12: -0.0021 REMARK 3 T13: 0.0644 T23: -0.0209 REMARK 3 L TENSOR REMARK 3 L11: 5.0643 L22: 4.1886 REMARK 3 L33: 0.9227 L12: 3.2905 REMARK 3 L13: -0.0886 L23: -0.8534 REMARK 3 S TENSOR REMARK 3 S11: 0.0443 S12: 0.0801 S13: 0.1240 REMARK 3 S21: 0.2384 S22: 0.1839 S23: 0.3050 REMARK 3 S31: -0.2472 S32: 0.1572 S33: -0.2282 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4NV5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000083694. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 5.5 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-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27546 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.790 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.76200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PARROT REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG3350, 0.1M SODIUM CACODYLATE, REMARK 280 PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 70.42100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 59.41100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 70.42100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 59.41100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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 GLN A 16 REMARK 465 PHE A 49 REMARK 465 ALA A 50 REMARK 465 THR A 51 REMARK 465 GLY A 52 REMARK 465 ASP A 53 REMARK 465 GLY A 92 REMARK 465 ASP A 155 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 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 SER B 3 REMARK 465 TYR B 4 REMARK 465 LEU B 5 REMARK 465 LYS B 6 REMARK 465 LEU B 7 REMARK 465 LYS B 8 REMARK 465 ALA B 9 REMARK 465 GLN B 10 REMARK 465 GLU B 11 REMARK 465 GLU B 12 REMARK 465 PHE B 49 REMARK 465 ALA B 50 REMARK 465 THR B 51 REMARK 465 GLY B 52 REMARK 465 ASP B 53 REMARK 465 GLU B 280 REMARK 465 GLU B 281 REMARK 465 GLY B 282 REMARK 465 ARG B 283 REMARK 465 LEU B 284 REMARK 465 GLU B 285 REMARK 465 HIS B 286 REMARK 465 HIS B 287 REMARK 465 HIS B 288 REMARK 465 HIS B 289 REMARK 465 HIS B 290 REMARK 465 HIS B 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 93 CG CD1 CD2 REMARK 470 ARG B 17 CG CD NE CZ NH1 NH2 REMARK 470 HIS B 18 CG ND1 CD2 CE1 NE2 REMARK 470 LEU B 93 CG CD1 CD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NE2 GLN A 225 NE2 GLN A 225 2554 2.17 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 TRP A 64 -26.42 99.82 REMARK 500 TRP B 64 -24.74 96.65 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 610 U10 B 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 U10 B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NV2 RELATED DB: PDB REMARK 900 RELATED ID: 4NV6 RELATED DB: PDB REMARK 900 RELATED ID: 3KP9 RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN A DIFFERENT ELECTRON TRANSFER STATE REMARK 900 RELATED ID: 3KP8 RELATED DB: PDB DBREF 4NV5 A 1 283 UNP Q2JJF6 Q2JJF6_SYNJB 1 283 DBREF 4NV5 B 1 283 UNP Q2JJF6 Q2JJF6_SYNJB 1 283 SEQADV 4NV5 ALA A 50 UNP Q2JJF6 CYS 50 ENGINEERED MUTATION SEQADV 4NV5 LEU A 284 UNP Q2JJF6 EXPRESSION TAG SEQADV 4NV5 GLU A 285 UNP Q2JJF6 EXPRESSION TAG SEQADV 4NV5 HIS A 286 UNP Q2JJF6 EXPRESSION TAG SEQADV 4NV5 HIS A 287 UNP Q2JJF6 EXPRESSION TAG SEQADV 4NV5 HIS A 288 UNP Q2JJF6 EXPRESSION TAG SEQADV 4NV5 HIS A 289 UNP Q2JJF6 EXPRESSION TAG SEQADV 4NV5 HIS A 290 UNP Q2JJF6 EXPRESSION TAG SEQADV 4NV5 HIS A 291 UNP Q2JJF6 EXPRESSION TAG SEQADV 4NV5 ALA B 50 UNP Q2JJF6 CYS 50 ENGINEERED MUTATION SEQADV 4NV5 LEU B 284 UNP Q2JJF6 EXPRESSION TAG SEQADV 4NV5 GLU B 285 UNP Q2JJF6 EXPRESSION TAG SEQADV 4NV5 HIS B 286 UNP Q2JJF6 EXPRESSION TAG SEQADV 4NV5 HIS B 287 UNP Q2JJF6 EXPRESSION TAG SEQADV 4NV5 HIS B 288 UNP Q2JJF6 EXPRESSION TAG SEQADV 4NV5 HIS B 289 UNP Q2JJF6 EXPRESSION TAG SEQADV 4NV5 HIS B 290 UNP Q2JJF6 EXPRESSION TAG SEQADV 4NV5 HIS B 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 ALA THR GLY SEQRES 5 A 291 ASP GLY GLY CYS 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 SEQRES 1 B 291 MET ALA SER TYR LEU LYS LEU LYS ALA GLN GLU GLU THR SEQRES 2 B 291 TRP LEU GLN ARG HIS SER ARG LEU ILE LEU ALA ILE LEU SEQRES 3 B 291 ALA GLY LEU GLY SER LEU LEU THR ALA TYR LEU THR TYR SEQRES 4 B 291 THR LYS LEU THR GLU GLN PRO ALA ALA PHE ALA THR GLY SEQRES 5 B 291 ASP GLY GLY CYS ASP LEU VAL LEU SER SER ARG TRP ALA SEQRES 6 B 291 GLU PHE LEU GLY ILE PRO THR ALA ALA VAL GLY LEU LEU SEQRES 7 B 291 GLY PHE LEU GLY VAL LEU ALA LEU ALA VAL LEU PRO ASP SEQRES 8 B 291 GLY LEU PRO LEU VAL LYS ARG TRP ARG TRP PRO ALA LEU SEQRES 9 B 291 PHE GLY LEU VAL SER ALA MET THR ALA PHE GLU MET TYR SEQRES 10 B 291 MET LEU TYR LEU MET VAL ALA VAL LEU ARG GLN PHE CYS SEQRES 11 B 291 MET TYR CYS THR THR ALA ILE ILE LEU VAL ALA GLY LEU SEQRES 12 B 291 GLY LEU VAL THR VAL LEU GLY HIS ARG TRP LEU ASP GLY SEQRES 13 B 291 GLY LYS LEU ALA PHE SER TYR ILE LEU VAL ALA PHE LEU SEQRES 14 B 291 THR LEU VAL THR THR ILE GLY VAL TYR ALA ASN GLN VAL SEQRES 15 B 291 PRO PRO PRO SER PRO LEU ALA VAL GLY LEU ALA ALA HIS SEQRES 16 B 291 LEU ARG GLN ILE GLY GLY THR MET TYR GLY ALA TYR TRP SEQRES 17 B 291 CYS PRO HIS CYS GLN ASP GLN LYS GLU LEU PHE GLY ALA SEQRES 18 B 291 ALA PHE ASP GLN VAL PRO TYR VAL GLU CYS SER PRO ASN SEQRES 19 B 291 GLY PRO GLY THR PRO GLN ALA GLN GLU CYS THR GLU ALA SEQRES 20 B 291 GLY ILE THR SER TYR PRO THR TRP ILE ILE ASN GLY ARG SEQRES 21 B 291 THR TYR THR GLY VAL ARG SER LEU GLU ALA LEU ALA VAL SEQRES 22 B 291 ALA SER GLY TYR PRO LEU GLU GLU GLY ARG LEU GLU HIS SEQRES 23 B 291 HIS HIS HIS HIS HIS HET U10 A 501 33 HET U10 B 501 33 HETNAM U10 UBIQUINONE-10 HETSYN U10 COENZYME Q10 FORMUL 3 U10 2(C59 H90 O4) HELIX 1 1 ARG A 20 THR A 43 1 24 HELIX 2 2 GLY A 55 SER A 62 1 8 HELIX 3 3 THR A 72 LEU A 89 1 18 HELIX 4 4 LEU A 95 VAL A 125 1 31 HELIX 5 5 CYS A 130 LEU A 149 1 20 HELIX 6 6 GLY A 157 VAL A 182 1 26 HELIX 7 7 SER A 186 GLY A 200 1 15 HELIX 8 8 CYS A 209 GLY A 220 1 12 HELIX 9 9 ALA A 221 VAL A 226 5 6 HELIX 10 10 ALA A 241 ALA A 247 1 7 HELIX 11 11 SER A 267 GLY A 276 1 10 HELIX 12 12 TRP B 14 HIS B 18 1 5 HELIX 13 13 HIS B 18 THR B 43 1 26 HELIX 14 14 GLY B 55 LEU B 60 1 6 HELIX 15 15 THR B 72 LEU B 89 1 18 HELIX 16 16 LEU B 95 ALA B 124 1 30 HELIX 17 17 CYS B 130 LEU B 149 1 20 HELIX 18 18 GLY B 156 ASN B 180 1 25 HELIX 19 19 SER B 186 GLY B 200 1 15 HELIX 20 20 CYS B 209 GLY B 220 1 12 HELIX 21 21 ALA B 221 GLN B 225 5 5 HELIX 22 22 ALA B 241 GLY B 248 1 8 HELIX 23 23 SER B 267 GLY B 276 1 10 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 SHEET 1 C 2 GLU B 66 PHE B 67 0 SHEET 2 C 2 ILE B 70 PRO B 71 -1 O ILE B 70 N PHE B 67 SHEET 1 D 4 TYR B 228 GLU B 230 0 SHEET 2 D 4 THR B 202 GLY B 205 1 N MET B 203 O VAL B 229 SHEET 3 D 4 THR B 254 ILE B 257 -1 O THR B 254 N TYR B 204 SHEET 4 D 4 ARG B 260 THR B 263 -1 O TYR B 262 N TRP B 255 SSBOND 1 CYS A 56 CYS A 130 1555 1555 2.04 SSBOND 2 CYS A 209 CYS A 212 1555 1555 2.04 SSBOND 3 CYS A 231 CYS A 244 1555 1555 2.03 SSBOND 4 CYS B 56 CYS B 130 1555 1555 2.04 SSBOND 5 CYS B 209 CYS B 212 1555 1555 2.04 SSBOND 6 CYS B 231 CYS B 244 1555 1555 2.03 CISPEP 1 TYR A 252 PRO A 253 0 -2.36 CISPEP 2 TYR B 252 PRO B 253 0 -0.53 SITE 1 AC1 13 VAL A 59 LEU A 60 SER A 62 TRP A 64 SITE 2 AC1 13 ALA A 65 THR A 72 VAL A 75 GLY A 76 SITE 3 AC1 13 PHE A 114 GLU A 115 MET A 118 MET A 122 SITE 4 AC1 13 CYS A 133 SITE 1 AC2 14 THR B 34 VAL B 59 LEU B 60 ALA B 65 SITE 2 AC2 14 THR B 72 VAL B 75 GLY B 76 ALA B 110 SITE 3 AC2 14 PHE B 114 GLU B 115 MET B 118 LEU B 121 SITE 4 AC2 14 MET B 122 CYS B 133 CRYST1 140.842 118.822 68.034 90.00 89.85 90.00 C 1 2 1 8 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 0.007100 0.000000 -0.000019 0.00000 SCALE2 0.000000 0.008416 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014699 0.00000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 -0.984315 -0.174570 -0.025462 -71.13413 1 MTRIX2 2 0.174490 -0.984644 0.005363 35.26907 1 MTRIX3 2 -0.026007 0.000836 0.999661 -35.06409 1