HEADER ELECTRON TRANSPORT/OXIDOREDUCTASE 09-APR-12 3VRD TITLE CRYSTAL STRUCTURE OF FLAVOCYTOCHROME C FROM THERMOCHROMATIUM TEPIDUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: FLAVOCYTOCHROME C HEME SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FCCA SUBUNIT; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: FLAVOCYTOCHROME C FLAVIN SUBUNIT; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: FCCB SUBUNIT SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCHROMATIUM TEPIDUM; SOURCE 3 ORGANISM_TAXID: 1050; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: THERMOCHROMATIUM TEPIDUM; SOURCE 6 ORGANISM_TAXID: 1050 KEYWDS SULFIDE OXIDATION, HEME C BINDING, FAD BINDING, ELECTRON TRANSPORT- KEYWDS 2 OXIDOREDUCTASE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.HIRANO,Y.KIMURA,H.SUZUKI,K.MIKI,Z.-Y.WANG REVDAT 5 25-DEC-24 3VRD 1 REMARK LINK REVDAT 4 06-DEC-23 3VRD 1 REMARK REVDAT 3 08-NOV-23 3VRD 1 REMARK LINK REVDAT 2 22-NOV-17 3VRD 1 REMARK LINK REVDAT 1 12-SEP-12 3VRD 0 JRNL AUTH Y.HIRANO,Y.KIMURA,H.SUZUKI,K.MIKI,Z.-Y.WANG JRNL TITL STRUCTURE ANALYSIS AND COMPARATIVE CHARACTERIZATION OF THE JRNL TITL 2 CYTOCHROME C' AND FLAVOCYTOCHROME C FROM THERMOPHILIC PURPLE JRNL TITL 3 PHOTOSYNTHETIC BACTERIUM THERMOCHROMATIUM TEPIDUM JRNL REF BIOCHEMISTRY V. 51 6556 2012 JRNL REFN ISSN 0006-2960 JRNL PMID 22827326 JRNL DOI 10.1021/BI3005522 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 79955 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) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4208 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5146 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.58 REMARK 3 BIN R VALUE (WORKING SET) : 0.2230 REMARK 3 BIN FREE R VALUE SET COUNT : 260 REMARK 3 BIN FREE R VALUE : 0.2650 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4379 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 165 REMARK 3 SOLVENT ATOMS : 553 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : -0.05000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.073 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.077 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.046 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.228 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4672 ; 0.029 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6371 ; 2.744 ; 2.008 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 574 ; 6.584 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 191 ;33.668 ;24.607 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 728 ;13.303 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;18.974 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 669 ; 0.198 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3585 ; 0.022 ; 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 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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: NULL REMARK 4 REMARK 4 3VRD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000095405. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 84166 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.27800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1FCD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 3000, 0.2M POTASSIUM NITRATE, REMARK 280 0.05M MES-NAOH, PH 6.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,Z+1/2 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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 70.30850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 70.30850 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 28.86000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 70.30850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 70.30850 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.86000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 70.30850 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 70.30850 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 28.86000 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 70.30850 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 70.30850 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 28.86000 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: 8050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -73.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 ALA B 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 960 O HOH B 961 1.69 REMARK 500 O HOH B 781 O HOH B 966 1.82 REMARK 500 SG CYS A 101 CBB HEC A 202 1.86 REMARK 500 O1D HEC A 202 O HOH A 455 1.86 REMARK 500 O HOH B 943 O HOH B 944 1.89 REMARK 500 O HOH B 942 O HOH B 944 2.01 REMARK 500 O HOH B 687 O HOH B 922 2.02 REMARK 500 SG CYS B 42 C8M FAD B 501 2.03 REMARK 500 SG CYS A 11 CAB HEC A 201 2.06 REMARK 500 SG CYS A 14 CAC HEC A 201 2.09 REMARK 500 O HOH B 942 O HOH B 958 2.10 REMARK 500 SG CYS A 104 CAC HEC A 202 2.11 REMARK 500 NH2 ARG B 66 O HOH B 828 2.12 REMARK 500 O HOH B 960 O HOH B 962 2.14 REMARK 500 O HOH B 715 O HOH B 918 2.17 REMARK 500 SD CSS B 161 SD CSS B 337 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 5 CD GLU A 5 OE1 0.079 REMARK 500 TYR B 43 CG TYR B 43 CD2 0.092 REMARK 500 TYR B 166 CE1 TYR B 166 CZ 0.081 REMARK 500 GLY B 329 N GLY B 329 CA 0.096 REMARK 500 GLU B 363 CD GLU B 363 OE2 -0.067 REMARK 500 TRP B 379 CE2 TRP B 379 CD2 0.080 REMARK 500 ARG B 383 CZ ARG B 383 NH2 0.079 REMARK 500 REMARK 500 REMARK: NULL 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 LEU A 7 CB - CG - CD1 ANGL. DEV. = -11.1 DEGREES REMARK 500 ARG A 130 NE - CZ - NH1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG A 130 NE - CZ - NH2 ANGL. DEV. = -7.8 DEGREES REMARK 500 ASP A 135 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ARG A 137 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG A 140 CB - CG - CD ANGL. DEV. = 22.9 DEGREES REMARK 500 ARG A 140 CD - NE - CZ ANGL. DEV. = 20.5 DEGREES REMARK 500 ARG A 140 NE - CZ - NH1 ANGL. DEV. = 17.3 DEGREES REMARK 500 ARG A 140 NE - CZ - NH2 ANGL. DEV. = -15.1 DEGREES REMARK 500 ARG A 141 NE - CZ - NH2 ANGL. DEV. = -5.7 DEGREES REMARK 500 LEU A 154 CB - CG - CD1 ANGL. DEV. = -13.8 DEGREES REMARK 500 ARG B 53 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ASP B 63 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG B 66 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 LEU B 124 CB - CG - CD2 ANGL. DEV. = 10.4 DEGREES REMARK 500 ARG B 138 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 TYR B 338 CB - CG - CD1 ANGL. DEV. = -4.5 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 ALA A 25 -34.80 -136.15 REMARK 500 ILE A 53 -17.46 -149.71 REMARK 500 MET B 44 -0.47 65.01 REMARK 500 LYS B 85 66.72 60.17 REMARK 500 CSS B 161 79.99 60.16 REMARK 500 ASN B 269 -163.17 -120.22 REMARK 500 THR B 372 129.44 -39.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 477 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH B 953 DISTANCE = 5.90 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 15 NE2 REMARK 620 2 HEC A 201 NA 88.6 REMARK 620 3 HEC A 201 NB 90.7 90.7 REMARK 620 4 HEC A 201 NC 90.2 178.8 89.6 REMARK 620 5 HEC A 201 ND 90.3 89.6 178.9 90.1 REMARK 620 6 MET A 54 SD 176.5 94.8 89.3 86.3 89.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 202 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 105 NE2 REMARK 620 2 HEC A 202 NA 89.3 REMARK 620 3 HEC A 202 NB 89.9 91.2 REMARK 620 4 HEC A 202 NC 89.5 178.8 88.6 REMARK 620 5 HEC A 202 ND 91.2 87.9 178.6 92.3 REMARK 620 6 MET A 147 SD 175.1 92.0 94.8 89.2 84.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 B 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VRC RELATED DB: PDB DBREF 3VRD A 1 174 UNP D0G7Q3 D0G7Q3_THETI 26 199 DBREF 3VRD B 1 401 UNP D0G7Q4 D0G7Q4_THETI 31 431 SEQRES 1 A 174 GLU PRO THR ALA GLU MET LEU ALA ASN ASN CYS ALA GLY SEQRES 2 A 174 CYS HIS GLY THR ARG GLY ASN SER ALA GLY PRO ALA SER SEQRES 3 A 174 PRO SER ILE ALA GLN MET ASP PRO ALA VAL PHE VAL GLU SEQRES 4 A 174 VAL MET GLU GLN PHE LYS SER GLY GLU ILE GLN SER THR SEQRES 5 A 174 ILE MET GLY ARG ILE ALA LYS GLY TYR SER THR ALA ASP SEQRES 6 A 174 PHE GLN LYS MET ALA GLU TYR PHE LYS GLN GLN THR TYR SEQRES 7 A 174 GLN PRO VAL LYS GLN SER PHE ASP LYS ALA LEU VAL ALA SEQRES 8 A 174 LYS GLY THR LYS LEU HIS ASP LYS TYR CYS GLU LYS CYS SEQRES 9 A 174 HIS VAL GLU SER GLY LYS PRO LEU ALA ASP GLN ASP GLU SEQRES 10 A 174 TYR HIS ILE LEU ALA GLY GLN TRP THR PRO TYR LEU ARG SEQRES 11 A 174 TYR ALA ILE GLU ASP PHE ARG ALA GLU ARG ARG PRO MET SEQRES 12 A 174 GLU LYS LYS MET ALA SER LYS LEU LYS GLU LEU LEU LYS SEQRES 13 A 174 ALA GLU GLY GLU ASP GLY LEU ASP ALA LEU PHE ALA PHE SEQRES 14 A 174 TYR ALA SER GLN GLN SEQRES 1 B 401 ALA GLY ARG LYS VAL VAL VAL VAL GLY GLY GLY THR GLY SEQRES 2 B 401 GLY ALA THR ALA ALA LYS TYR ILE LYS LEU ALA ASP PRO SEQRES 3 B 401 SER ILE GLU VAL THR LEU ILE GLU PRO ASN GLU THR TYR SEQRES 4 B 401 TYR THR CYS TYR MET SER ASN GLU VAL ILE GLY GLY ASP SEQRES 5 B 401 ARG GLU LEU ALA SER LEU ARG VAL GLY TYR ASP GLY LEU SEQRES 6 B 401 ARG ALA HIS GLY ILE GLN VAL VAL HIS ASP SER ALA LEU SEQRES 7 B 401 GLY ILE ASP PRO ASP LYS LYS LEU VAL LYS THR ALA GLY SEQRES 8 B 401 GLY ALA GLU PHE ALA TYR ASP ARG CYS VAL VAL ALA PRO SEQRES 9 B 401 GLY ILE ASP LEU LEU TYR ASP LYS ILE GLU GLY TYR SER SEQRES 10 B 401 GLU ALA LEU ALA ALA LYS LEU PRO HIS ALA TRP LYS ALA SEQRES 11 B 401 GLY GLU GLN THR ALA LEU LEU ARG ARG GLN LEU GLU SER SEQRES 12 B 401 MET ASP ASP GLY GLY VAL VAL ILE ILE ALA PRO PRO ALA SEQRES 13 B 401 PRO PRO PHE ARG CSS PRO PRO GLY PRO TYR GLU ARG ALA SEQRES 14 B 401 SER GLN ILE ALA HIS TYR LEU LYS ALA HIS LYS SER LYS SEQRES 15 B 401 SER LYS VAL ILE ILE LEU ASP ASN SER GLN THR PHE SER SEQRES 16 B 401 LYS GLN ALA GLN PHE THR LYS GLY TRP GLU ARG LEU TYR SEQRES 17 B 401 GLY PHE GLY THR GLU ASN ALA LEU ILE GLU TRP HIS PRO SEQRES 18 B 401 GLY PRO ASP ALA ALA VAL VAL LYS THR ASP THR GLU ALA SEQRES 19 B 401 MET THR VAL GLU THR SER PHE GLY GLU THR PHE LYS ALA SEQRES 20 B 401 ALA VAL ILE ASN LEU ILE PRO PRO GLN ARG ALA GLY LYS SEQRES 21 B 401 ILE ALA GLN SER ALA SER LEU THR ASN ASP SER GLY TRP SEQRES 22 B 401 CYS PRO VAL ASP ILE ARG THR PHE GLU SER SER LEU GLN SEQRES 23 B 401 PRO GLY ILE HIS VAL ILE GLY ASP ALA CYS ASN ALA ALA SEQRES 24 B 401 PRO MET PRO LYS SER ALA TYR SER ALA ASN SER GLN ALA SEQRES 25 B 401 LYS VAL ALA ALA ALA ALA VAL VAL ALA LEU LEU LYS GLY SEQRES 26 B 401 GLU GLU PRO GLY THR PRO SER TYR LEU ASN THR CSS TYR SEQRES 27 B 401 SER ILE LEU ALA PRO GLY TYR GLY ILE SER ILE ALA ALA SEQRES 28 B 401 VAL TYR ARG PRO ASN ALA GLU GLY LYS ALA ILE GLU ALA SEQRES 29 B 401 VAL PRO ASP SER GLY GLY ILE THR PRO VAL ASP ALA PRO SEQRES 30 B 401 ASP TRP VAL LEU GLU ARG GLU VAL GLN TYR ALA HIS SER SEQRES 31 B 401 TRP TYR ASN ASN ILE VAL HIS ASP THR PHE GLY MODRES 3VRD CSS B 161 CYS S-MERCAPTOCYSTEINE MODRES 3VRD CSS B 337 CYS S-MERCAPTOCYSTEINE HET CSS B 161 7 HET CSS B 337 7 HET HEC A 201 43 HET HEC A 202 47 HET GOL A 203 6 HET GOL A 204 6 HET NO3 A 205 4 HET FAD B 501 53 HET GOL B 502 6 HET NO3 B 503 4 HETNAM CSS S-MERCAPTOCYSTEINE HETNAM HEC HEME C HETNAM GOL GLYCEROL HETNAM NO3 NITRATE ION HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 CSS 2(C3 H7 N O2 S2) FORMUL 3 HEC 2(C34 H34 FE N4 O4) FORMUL 5 GOL 3(C3 H8 O3) FORMUL 7 NO3 2(N O3 1-) FORMUL 8 FAD C27 H33 N9 O15 P2 FORMUL 11 HOH *553(H2 O) HELIX 1 1 THR A 3 ASN A 9 1 7 HELIX 2 2 CYS A 11 GLY A 16 1 6 HELIX 3 3 THR A 17 ASN A 20 5 4 HELIX 4 4 ASP A 33 GLY A 47 1 15 HELIX 5 5 ILE A 53 LYS A 59 1 7 HELIX 6 6 SER A 62 GLN A 76 1 15 HELIX 7 7 ASP A 86 ALA A 88 5 3 HELIX 8 8 LEU A 89 CYS A 101 1 13 HELIX 9 9 HIS A 105 LYS A 110 5 6 HELIX 10 10 TRP A 125 ALA A 138 1 14 HELIX 11 11 GLU A 144 GLN A 173 1 30 HELIX 12 12 GLY B 11 ASP B 25 1 15 HELIX 13 13 MET B 44 GLY B 51 1 8 HELIX 14 14 GLU B 54 SER B 57 5 4 HELIX 15 15 TYR B 62 HIS B 68 1 7 HELIX 16 16 TYR B 110 ILE B 113 5 4 HELIX 17 17 GLU B 118 LYS B 123 5 6 HELIX 18 18 GLY B 131 MET B 144 1 14 HELIX 19 19 PRO B 163 LYS B 180 1 18 HELIX 20 20 LYS B 196 TYR B 208 1 13 HELIX 21 21 GLY B 259 ALA B 265 1 7 HELIX 22 22 GLY B 293 CYS B 296 5 4 HELIX 23 23 SER B 304 GLY B 325 1 22 HELIX 24 24 PRO B 377 GLY B 401 1 25 SHEET 1 A 5 GLN B 71 VAL B 73 0 SHEET 2 A 5 GLU B 29 ILE B 33 1 N LEU B 32 O GLN B 71 SHEET 3 A 5 LYS B 4 VAL B 8 1 N VAL B 5 O GLU B 29 SHEET 4 A 5 ARG B 99 VAL B 102 1 O VAL B 101 N VAL B 8 SHEET 5 A 5 ILE B 289 VAL B 291 1 O HIS B 290 N VAL B 102 SHEET 1 B 2 TYR B 39 TYR B 40 0 SHEET 2 B 2 ARG B 59 VAL B 60 -1 O VAL B 60 N TYR B 39 SHEET 1 C 3 ALA B 77 ASP B 81 0 SHEET 2 C 3 LEU B 86 THR B 89 -1 O LYS B 88 N LEU B 78 SHEET 3 C 3 GLU B 94 ALA B 96 -1 O PHE B 95 N VAL B 87 SHEET 1 D 2 ILE B 106 LEU B 108 0 SHEET 2 D 2 GLN B 256 ALA B 258 -1 O ARG B 257 N ASP B 107 SHEET 1 E 4 ILE B 217 HIS B 220 0 SHEET 2 E 4 LYS B 184 LEU B 188 1 N ILE B 187 O GLU B 218 SHEET 3 E 4 VAL B 149 ALA B 153 1 N VAL B 150 O ILE B 186 SHEET 4 E 4 VAL B 249 LEU B 252 1 O ASN B 251 N ILE B 151 SHEET 1 F 3 VAL B 227 ASP B 231 0 SHEET 2 F 3 THR B 236 THR B 239 -1 O GLU B 238 N LYS B 229 SHEET 3 F 3 THR B 244 LYS B 246 -1 O PHE B 245 N VAL B 237 SHEET 1 G 3 TYR B 333 ALA B 342 0 SHEET 2 G 3 TYR B 345 PRO B 355 -1 O TYR B 345 N LEU B 341 SHEET 3 G 3 ILE B 362 ALA B 364 -1 O GLU B 363 N ARG B 354 SHEET 1 H 3 TYR B 333 ALA B 342 0 SHEET 2 H 3 TYR B 345 PRO B 355 -1 O TYR B 345 N LEU B 341 SHEET 3 H 3 GLY B 370 ILE B 371 -1 O GLY B 370 N ALA B 350 LINK SG CYS A 101 CAB HEC A 202 1555 1555 1.93 LINK C ARG B 160 N CSS B 161 1555 1555 1.32 LINK C CSS B 161 N PRO B 162 1555 1555 1.32 LINK C THR B 336 N CSS B 337 1555 1555 1.31 LINK C CSS B 337 N TYR B 338 1555 1555 1.32 LINK NE2 HIS A 15 FE HEC A 201 1555 1555 1.99 LINK SD MET A 54 FE HEC A 201 1555 1555 2.31 LINK NE2 HIS A 105 FE HEC A 202 1555 1555 2.02 LINK SD MET A 147 FE HEC A 202 1555 1555 2.38 CISPEP 1 GLY A 23 PRO A 24 0 18.43 CISPEP 2 PRO B 157 PRO B 158 0 6.57 CISPEP 3 GLY B 222 PRO B 223 0 3.67 CISPEP 4 ALA B 299 PRO B 300 0 10.05 SITE 1 AC1 22 CYS A 11 CYS A 14 HIS A 15 PHE A 37 SITE 2 AC1 22 VAL A 40 MET A 41 PHE A 44 SER A 51 SITE 3 AC1 22 THR A 52 ILE A 53 MET A 54 MET A 69 SITE 4 AC1 22 TYR A 128 HEC A 202 GOL A 203 HOH A 320 SITE 5 AC1 22 TYR B 306 LEU B 334 THR B 336 TYR B 338 SITE 6 AC1 22 TYR B 387 HOH B 601 SITE 1 AC2 21 TYR A 100 CYS A 101 CYS A 104 HIS A 105 SITE 2 AC2 21 HIS A 119 LEU A 121 TYR A 128 PHE A 136 SITE 3 AC2 21 ARG A 141 MET A 143 GLU A 144 LYS A 146 SITE 4 AC2 21 MET A 147 LEU A 154 HEC A 201 HOH A 302 SITE 5 AC2 21 HOH A 307 HOH A 337 HOH A 380 HOH A 455 SITE 6 AC2 21 HOH A 478 SITE 1 AC3 8 PHE A 44 TYR A 128 ALA A 132 ASP A 135 SITE 2 AC3 8 ARG A 141 HEC A 201 ARG B 383 HOH B 601 SITE 1 AC4 7 PRO A 2 GLY A 60 ASP A 65 HOH A 301 SITE 2 AC4 7 HOH A 390 HOH A 428 VAL B 365 SITE 1 AC5 6 ARG A 137 LEU A 155 GLU B 54 ALA B 56 SITE 2 AC5 6 SER B 57 HOH B 793 SITE 1 AC6 44 VAL B 8 GLY B 9 GLY B 11 THR B 12 SITE 2 AC6 44 GLY B 13 ILE B 33 GLU B 34 PRO B 35 SITE 3 AC6 44 ASN B 36 TYR B 39 CYS B 42 TYR B 43 SITE 4 AC6 44 SER B 76 ALA B 77 ALA B 103 PRO B 104 SITE 5 AC6 44 GLY B 105 TRP B 128 ARG B 160 CSS B 161 SITE 6 AC6 44 ARG B 168 ILE B 261 GLY B 293 ASP B 294 SITE 7 AC6 44 LYS B 303 SER B 304 ALA B 305 TYR B 306 SITE 8 AC6 44 ALA B 308 TYR B 338 TRP B 391 HOH B 602 SITE 9 AC6 44 HOH B 603 HOH B 604 HOH B 618 HOH B 667 SITE 10 AC6 44 HOH B 683 HOH B 700 HOH B 709 HOH B 715 SITE 11 AC6 44 HOH B 722 HOH B 765 HOH B 908 HOH B 959 SITE 1 AC7 7 ALA A 138 ARG A 140 HOH A 330 LEU B 55 SITE 2 AC7 7 GLU B 142 HOH B 609 HOH B 627 SITE 1 AC8 7 LEU B 207 ALA B 342 PRO B 343 GLY B 344 SITE 2 AC8 7 TYR B 345 HOH B 920 HOH B 941 CRYST1 140.617 140.617 57.720 90.00 90.00 90.00 I 4 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 0.007112 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007112 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017325 0.00000