HEADER OXIDOREDUCTASE 10-OCT-14 4V2K TITLE CRYSTAL STRUCTURE OF THE THIOSULFATE DEHYDROGENASE TSDA IN COMPLEX TITLE 2 WITH THIOSULFATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOSULFATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.8.2.2; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: PERSULFIDE MODIFICATION ON C123 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ALLOCHROMATIUM VINOSUM; SOURCE 3 ORGANISM_TAXID: 1049; SOURCE 4 ATCC: 17899; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: L56; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PQE80L KEYWDS OXIDOREDUCTASE, CYTOCHROME C, HIS/CYS HEME, DISULFIDE FORMATION, KEYWDS 2 CYSTEINE MODIFICATION EXPDTA X-RAY DIFFRACTION AUTHOR D.B.GRABARCZYK,P.E.CHAPPELL,B.EISEL,S.JOHNSON,S.M.LEA,B.C.BERKS REVDAT 5 06-NOV-24 4V2K 1 REMARK REVDAT 4 10-JAN-24 4V2K 1 REMARK LINK REVDAT 3 25-SEP-19 4V2K 1 COMPND REMARK HET HETNAM REVDAT 3 2 1 HETSYN FORMUL LINK SITE REVDAT 3 3 1 ATOM REVDAT 2 22-JUL-15 4V2K 1 JRNL REVDAT 1 18-FEB-15 4V2K 0 JRNL AUTH D.B.GRABARCZYK,P.E.CHAPPELL,B.EISEL,S.JOHNSON,S.M.LEA, JRNL AUTH 2 B.C.BERKS JRNL TITL MECHANISM OF THIOSULFATE OXIDATION IN THE SOXA FAMILY OF JRNL TITL 2 CYSTEINE-LIGATED CYTOCHROMES JRNL REF J.BIOL.CHEM. V. 290 9209 2015 JRNL REFN ISSN 0021-9258 JRNL PMID 25673696 JRNL DOI 10.1074/JBC.M114.618025 REMARK 2 REMARK 2 RESOLUTION. 1.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 1.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 56552 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) : 0.143 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.155 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3003 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) : 1.29 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.32 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3804 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.2260 REMARK 3 BIN FREE R VALUE SET COUNT : 215 REMARK 3 BIN FREE R VALUE : 0.2430 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1755 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 91 REMARK 3 SOLVENT ATOMS : 201 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.92 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.56000 REMARK 3 B22 (A**2) : 1.29000 REMARK 3 B33 (A**2) : -0.23000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.11000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.039 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.040 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.034 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.721 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.981 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.979 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1951 ; 0.029 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1786 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2677 ; 2.411 ; 2.027 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4084 ; 1.553 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 244 ; 6.072 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 81 ;26.375 ;22.346 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 265 ;11.846 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;18.701 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 274 ; 0.165 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2270 ; 0.018 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 478 ; 0.017 ; 0.020 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): 952 ; 1.600 ; 1.244 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 951 ; 1.581 ; 1.240 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1192 ; 2.409 ; 1.863 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 999 ; 2.691 ; 1.527 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 : 1 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 31 A 265 REMARK 3 ORIGIN FOR THE GROUP (A): -19.2128 2.8352 4.4805 REMARK 3 T TENSOR REMARK 3 T11: 0.0117 T22: 0.0869 REMARK 3 T33: 0.0036 T12: 0.0009 REMARK 3 T13: -0.0032 T23: 0.0028 REMARK 3 L TENSOR REMARK 3 L11: 3.0726 L22: 0.4212 REMARK 3 L33: 0.9722 L12: 0.4738 REMARK 3 L13: -0.5928 L23: -0.0099 REMARK 3 S TENSOR REMARK 3 S11: 0.0593 S12: -0.1188 S13: -0.0010 REMARK 3 S21: 0.0418 S22: -0.0498 S23: -0.0354 REMARK 3 S31: -0.0832 S32: -0.0575 S33: -0.0095 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 ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 4V2K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-OCT-14. REMARK 100 THE DEPOSITION ID IS D_1290061880. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.920 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS THROUGH XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS THROUGH XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60432 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.290 REMARK 200 RESOLUTION RANGE LOW (A) : 44.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.48000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 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: PDB ENTRIES 1H32 AND 2ZOO REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MM AMMONIUM ACETATE, 7.5% PEG 10K REMARK 280 PH 4.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 39.64000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.21000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 39.64000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.21000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 7220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -123.1 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 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2146 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2159 LIES ON A SPECIAL POSITION. 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 GLU A 28 REMARK 465 GLU A 29 REMARK 465 PRO A 30 REMARK 465 GLU A 266 REMARK 465 PRO A 267 REMARK 465 THR A 268 REMARK 465 GLY A 269 REMARK 465 ASP A 270 REMARK 465 ALA A 271 REMARK 465 SER A 272 REMARK 465 TRP A 273 REMARK 465 SER A 274 REMARK 465 HIS A 275 REMARK 465 PRO A 276 REMARK 465 GLN A 277 REMARK 465 PHE A 278 REMARK 465 GLU A 279 REMARK 465 LYS A 280 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 ALA A 41 CB REMARK 470 GLU A 173 OE2 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 GLU A 173 O HOH A 2147 1.43 REMARK 500 OD1 ASP A 200 OD1 ASP A 202 1.43 REMARK 500 O HOH A 2008 O HOH A 2009 1.68 REMARK 500 O HOH A 2162 O HOH A 2164 1.90 REMARK 500 O HOH A 2049 O HOH A 2050 1.99 REMARK 500 O HOH A 2129 O HOH A 2130 2.09 REMARK 500 CG ASP A 200 OD1 ASP A 202 2.13 REMARK 500 O HOH A 2154 O HOH A 2162 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 O HOH A 2160 O HOH A 2160 2455 1.59 REMARK 500 O HOH A 2106 O HOH A 2106 2555 1.67 REMARK 500 O HOH A 2105 O HOH A 2106 2555 2.09 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 TYR A 146 CZ TYR A 146 CE2 -0.081 REMARK 500 TYR A 205 CZ TYR A 205 CE2 -0.083 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 ARG A 56 NE - CZ - NH2 ANGL. DEV. = -5.1 DEGREES REMARK 500 ARG A 102 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 102 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 GLU A 117 OE1 - CD - OE2 ANGL. DEV. = -8.2 DEGREES REMARK 500 ARG A 126 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 LEU A 128 CB - CG - CD1 ANGL. DEV. = 13.2 DEGREES REMARK 500 ASP A 194 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 202 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 204 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 214 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ASP A 242 CB - CG - OD1 ANGL. DEV. = -6.5 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 ASP A 45 -156.33 -90.72 REMARK 500 ASP A 61 44.54 -144.93 REMARK 500 ARG A 126 -70.30 -109.11 REMARK 500 ARG A 172 141.63 124.52 REMARK 500 PRO A 237 150.78 -46.54 REMARK 500 REMARK 500 REMARK: NULL 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 601 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 80 NE2 REMARK 620 2 HEC A 601 NA 90.0 REMARK 620 3 HEC A 601 NB 89.5 90.6 REMARK 620 4 HEC A 601 NC 91.2 178.8 89.4 REMARK 620 5 HEC A 601 ND 92.2 89.5 178.2 90.5 REMARK 620 6 CSS A 123 SD 178.1 91.4 89.1 87.5 89.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 600 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 191 NE2 REMARK 620 2 HEC A 600 NA 90.1 REMARK 620 3 HEC A 600 NB 88.4 89.4 REMARK 620 4 HEC A 600 NC 89.3 179.2 90.0 REMARK 620 5 HEC A 600 ND 92.4 89.8 178.8 90.8 REMARK 620 6 MET A 236 SD 173.5 95.7 88.7 84.9 90.6 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 HEM A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE THJ A 700 DBREF 4V2K A 28 270 UNP D3RVD4 TSDA_ALLVD 28 270 SEQADV 4V2K ALA A 271 UNP D3RVD4 EXPRESSION TAG SEQADV 4V2K SER A 272 UNP D3RVD4 EXPRESSION TAG SEQADV 4V2K TRP A 273 UNP D3RVD4 EXPRESSION TAG SEQADV 4V2K SER A 274 UNP D3RVD4 EXPRESSION TAG SEQADV 4V2K HIS A 275 UNP D3RVD4 EXPRESSION TAG SEQADV 4V2K PRO A 276 UNP D3RVD4 EXPRESSION TAG SEQADV 4V2K GLN A 277 UNP D3RVD4 EXPRESSION TAG SEQADV 4V2K PHE A 278 UNP D3RVD4 EXPRESSION TAG SEQADV 4V2K GLU A 279 UNP D3RVD4 EXPRESSION TAG SEQADV 4V2K LYS A 280 UNP D3RVD4 EXPRESSION TAG SEQRES 1 A 253 GLU GLU PRO PRO THR VAL ALA LEU THR VAL PRO ALA ALA SEQRES 2 A 253 ALA LEU LEU PRO ASP GLY ALA LEU GLY GLU SER ILE VAL SEQRES 3 A 253 ARG GLY ARG ARG TYR LEU SER ASP THR PRO ALA GLN LEU SEQRES 4 A 253 PRO ASP PHE VAL GLY ASN GLY LEU ALA CYS ARG HIS CYS SEQRES 5 A 253 HIS PRO GLY ARG ASP GLY GLU VAL GLY THR GLU ALA ASN SEQRES 6 A 253 ALA ALA PRO PHE VAL GLY VAL VAL GLY ARG PHE PRO GLN SEQRES 7 A 253 TYR SER ALA ARG HIS GLY ARG LEU ILE THR LEU GLU GLN SEQRES 8 A 253 ARG ILE GLY ASP CSS PHE GLU ARG SER LEU ASN GLY ARG SEQRES 9 A 253 ALA LEU ALA LEU ASP HIS PRO ALA LEU ILE ASP MET LEU SEQRES 10 A 253 ALA TYR MET SER TRP LEU SER GLN GLY VAL PRO VAL GLY SEQRES 11 A 253 ALA VAL VAL ALA GLY HIS GLY ILE PRO THR LEU THR LEU SEQRES 12 A 253 GLU ARG GLU PRO ASP GLY VAL HIS GLY GLU ALA LEU TYR SEQRES 13 A 253 GLN ALA ARG CYS LEU ALA CYS HIS GLY ALA ASP GLY SER SEQRES 14 A 253 GLY THR LEU ASP ALA ASP GLY ARG TYR LEU PHE PRO PRO SEQRES 15 A 253 LEU TRP GLY PRO ARG SER PHE ASN THR GLY ALA GLY MET SEQRES 16 A 253 ASN ARG GLN ALA THR ALA ALA GLY PHE ILE LYS HIS LYS SEQRES 17 A 253 MET PRO LEU GLY ALA ASP ASP SER LEU SER ASP GLU GLU SEQRES 18 A 253 ALA TRP ASP VAL ALA GLY PHE VAL LEU THR HIS PRO ARG SEQRES 19 A 253 PRO LEU PHE GLN GLU PRO THR GLY ASP ALA SER TRP SER SEQRES 20 A 253 HIS PRO GLN PHE GLU LYS MODRES 4V2K CSS A 123 CYS S-MERCAPTOCYSTEINE HET CSS A 123 7 HET HEC A 600 43 HET HEC A 601 47 HET THJ A 700 5 HETNAM CSS S-MERCAPTOCYSTEINE HETNAM HEC HEME C HETNAM THJ THIOSULFATE FORMUL 1 CSS C3 H7 N O2 S2 FORMUL 2 HEC 2(C34 H34 FE N4 O4) FORMUL 4 THJ O3 S2 2- FORMUL 5 HOH *201(H2 O) HELIX 1 1 ALA A 39 LEU A 43 5 5 HELIX 2 2 ASP A 45 ASP A 61 1 17 HELIX 3 3 ASP A 61 LEU A 66 1 6 HELIX 4 4 ALA A 75 CYS A 79 5 5 HELIX 5 5 GLY A 98 PHE A 103 5 6 HELIX 6 6 THR A 115 ARG A 126 1 12 HELIX 7 7 HIS A 137 SER A 151 1 15 HELIX 8 8 ASP A 175 CYS A 187 1 13 HELIX 9 9 CYS A 187 GLY A 192 1 6 HELIX 10 10 ALA A 220 ASN A 223 5 4 HELIX 11 11 ARG A 224 MET A 236 1 13 HELIX 12 12 SER A 245 THR A 258 1 14 SHEET 1 AA 2 THR A 32 VAL A 33 0 SHEET 2 AA 2 VAL A 159 VAL A 160 1 O VAL A 159 N VAL A 33 SHEET 1 AB 2 GLN A 105 SER A 107 0 SHEET 2 AB 2 ARG A 112 ILE A 114 -1 O ARG A 112 N SER A 107 SHEET 1 AC 2 THR A 198 LEU A 199 0 SHEET 2 AC 2 TYR A 205 PHE A 207 -1 N LEU A 206 O THR A 198 LINK SG CYS A 76 CAB HEC A 601 1555 1555 1.81 LINK SG CYS A 79 CAC HEC A 601 1555 1555 1.86 LINK C ASP A 122 N CSS A 123 1555 1555 1.30 LINK C CSS A 123 N PHE A 124 1555 1555 1.33 LINK SG CYS A 187 CAB HEC A 600 1555 1555 1.79 LINK SG CYS A 190 CAC HEC A 600 1555 1555 1.90 LINK NE2 HIS A 80 FE HEC A 601 1555 1555 2.03 LINK SD CSS A 123 FE HEC A 601 1555 1555 2.31 LINK NE2 HIS A 191 FE HEC A 600 1555 1555 2.06 LINK SD MET A 236 FE HEC A 600 1555 1555 2.35 CISPEP 1 PHE A 103 PRO A 104 0 4.08 CISPEP 2 MET A 236 PRO A 237 0 -20.32 SITE 1 AC1 17 HIS A 78 PRO A 81 ARG A 186 CYS A 187 SITE 2 AC1 17 CYS A 190 HIS A 191 LEU A 206 PHE A 207 SITE 3 AC1 17 PRO A 208 PRO A 209 LEU A 210 PHE A 216 SITE 4 AC1 17 PHE A 231 MET A 236 PRO A 237 LEU A 238 SITE 5 AC1 17 HOH A2066 SITE 1 AC2 24 LEU A 59 ALA A 75 CYS A 76 CYS A 79 SITE 2 AC2 24 HIS A 80 PHE A 96 LEU A 116 ARG A 119 SITE 3 AC2 24 CSS A 123 PHE A 124 SER A 127 LEU A 128 SITE 4 AC2 24 GLY A 164 ILE A 165 GLU A 171 THR A 227 SITE 5 AC2 24 THJ A 700 HOH A2070 HOH A2071 HOH A2085 SITE 6 AC2 24 HOH A2086 HOH A2109 HOH A2139 HOH A2202 SITE 1 AC3 11 ARG A 109 ARG A 119 ASP A 122 CSS A 123 SITE 2 AC3 11 ARG A 126 SER A 127 GLY A 219 ALA A 220 SITE 3 AC3 11 GLY A 221 HEC A 601 HOH A2110 CRYST1 79.280 70.420 57.910 90.00 129.34 90.00 C 1 2 1 4 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 0.012614 0.000000 0.010339 0.00000 SCALE2 0.000000 0.014201 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022328 0.00000