HEADER OXIDOREDUCTASE 03-AUG-05 2AKJ TITLE STRUCTURE OF SPINACH NITRITE REDUCTASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FERREDOXIN--NITRITE REDUCTASE, CHLOROPLAST; COMPND 3 CHAIN: A; COMPND 4 EC: 1.7.7.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SPINACIA OLERACEA; SOURCE 3 ORGANISM_COMMON: SPINACH; SOURCE 4 ORGANISM_TAXID: 3562; SOURCE 5 GENE: NIR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET30B; SOURCE 10 OTHER_DETAILS: SPINACH NITRITE REDUCTASE WAS PRODUCED AS A HIS- SOURCE 11 TAGGED RECOMBINANT PROTEIN EXPRESSED FROM THE PET30B-NIR PLASMID IN SOURCE 12 E. COLI. THE E. COLI CELLS WERE CO-TRANSFORMED WITH THE PLASMID SOURCE 13 PKK233-CYSG THAT CONTAINS THE CYSG GENE ENCODING THE ENZYME THAT SOURCE 14 CATALYZES THE RATE-LIMITING STEP IN SIROHEME BIOSYNTHESIS. KEYWDS X-RAY CRYSTALLOGRAPHY; HEME; ELECTRON TRANSPORT, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR U.SWAMY,M.WANG,J.N.TRIPATHY,S.-K.KIM,M.HIRASAWA,D.B.KNAFF,J.P.ALLEN REVDAT 4 27-DEC-23 2AKJ 1 COMPND REMARK SEQADV FORMUL REVDAT 3 04-APR-18 2AKJ 1 REMARK REVDAT 2 24-FEB-09 2AKJ 1 VERSN REVDAT 1 24-JAN-06 2AKJ 0 JRNL AUTH U.SWAMY,M.WANG,J.N.TRIPATHY,S.K.KIM,M.HIRASAWA,D.B.KNAFF, JRNL AUTH 2 J.P.ALLEN JRNL TITL STRUCTURE OF SPINACH NITRITE REDUCTASE: IMPLICATIONS FOR JRNL TITL 2 MULTI-ELECTRON REACTIONS BY THE IRON-SULFUR:SIROHEME JRNL TITL 3 COFACTOR JRNL REF BIOCHEMISTRY V. 44 16054 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 16331965 JRNL DOI 10.1021/BI050981Y REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 24304 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) : 0.252 REMARK 3 R VALUE (WORKING SET) : 0.250 REMARK 3 FREE R VALUE : 0.300 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1300 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1749 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.4130 REMARK 3 BIN FREE R VALUE SET COUNT : 105 REMARK 3 BIN FREE R VALUE : 0.4970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4222 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 71 REMARK 3 SOLVENT ATOMS : 6 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.65000 REMARK 3 B22 (A**2) : -2.65000 REMARK 3 B33 (A**2) : 5.30000 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): 0.554 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.360 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.276 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.378 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.909 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.867 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4395 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5956 ; 1.749 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 534 ; 6.721 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 201 ;37.101 ;23.930 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 782 ;22.913 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 37 ;18.008 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 643 ; 0.123 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3325 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2235 ; 0.250 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2980 ; 0.322 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 164 ; 0.175 ; 0.200 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): 27 ; 0.235 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.095 ; 0.200 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): 2715 ; 0.493 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4307 ; 0.884 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2069 ; 1.236 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1635 ; 2.186 ; 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 : NULL 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: NULL REMARK 4 REMARK 4 2AKJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1000034002. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK, CRYSTALCLEAR REMARK 200 (MSC/RIGAKU) REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24304 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.12400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS HCL, POLYETHYLENE GLYCOL 4000, REMARK 280 MGCL2, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 60.47500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 64.48500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 64.48500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.23750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 64.48500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 64.48500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 90.71250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 64.48500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 64.48500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 30.23750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 64.48500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 64.48500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 90.71250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 60.47500 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 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 -45 REMARK 465 HIS A -44 REMARK 465 HIS A -43 REMARK 465 HIS A -42 REMARK 465 HIS A -41 REMARK 465 HIS A -40 REMARK 465 HIS A -39 REMARK 465 SER A -38 REMARK 465 SER A -37 REMARK 465 GLY A -36 REMARK 465 LEU A -35 REMARK 465 VAL A -34 REMARK 465 PRO A -33 REMARK 465 ARG A -32 REMARK 465 GLY A -31 REMARK 465 SER A -30 REMARK 465 GLY A -29 REMARK 465 MET A -28 REMARK 465 LYS A -27 REMARK 465 GLU A -26 REMARK 465 THR A -25 REMARK 465 ALA A -24 REMARK 465 ALA A -23 REMARK 465 ALA A -22 REMARK 465 LYS A -21 REMARK 465 PHE A -20 REMARK 465 GLU A -19 REMARK 465 ARG A -18 REMARK 465 GLN A -17 REMARK 465 HIS A -16 REMARK 465 MET A -15 REMARK 465 ASP A -14 REMARK 465 SER A -13 REMARK 465 PRO A -12 REMARK 465 ASP A -11 REMARK 465 LEU A -10 REMARK 465 GLY A -9 REMARK 465 THR A -8 REMARK 465 ASP A -7 REMARK 465 ASP A -6 REMARK 465 ASP A -5 REMARK 465 ASP A -4 REMARK 465 LYS A -3 REMARK 465 ALA A -2 REMARK 465 MET A -1 REMARK 465 GLY A 0 REMARK 465 CYS A 1 REMARK 465 GLN A 2 REMARK 465 LYS A 3 REMARK 465 ALA A 4 REMARK 465 VAL A 5 REMARK 465 SER A 6 REMARK 465 PRO A 7 REMARK 465 ALA A 8 REMARK 465 ALA A 9 REMARK 465 GLU A 10 REMARK 465 THR A 11 REMARK 465 ALA A 12 REMARK 465 ALA A 13 REMARK 465 VAL A 14 REMARK 465 SER A 15 REMARK 465 PRO A 16 REMARK 465 SER A 17 REMARK 465 VAL A 18 REMARK 465 ASP A 19 REMARK 465 ALA A 20 REMARK 465 ALA A 21 REMARK 465 GLU A 557 REMARK 465 ARG A 558 REMARK 465 GLU A 559 REMARK 465 GLU A 560 REMARK 465 ALA A 561 REMARK 465 GLU A 562 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 ASP A 31 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP A 85 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 VAL A 195 CB - CA - C ANGL. DEV. = -13.5 DEGREES REMARK 500 ASP A 298 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 347 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 379 CB - CG - OD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP A 503 CB - CG - OD2 ANGL. DEV. = 5.7 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 SER A 42 -77.13 -54.39 REMARK 500 LYS A 54 114.70 -171.95 REMARK 500 VAL A 88 -71.50 -135.55 REMARK 500 HIS A 102 33.93 -153.39 REMARK 500 TYR A 103 130.04 -24.87 REMARK 500 ASN A 114 -9.36 78.33 REMARK 500 LYS A 130 -48.47 -28.52 REMARK 500 GLN A 144 52.37 39.57 REMARK 500 SER A 170 5.23 53.59 REMARK 500 MET A 175 -92.41 -117.58 REMARK 500 ASP A 176 63.76 -109.63 REMARK 500 ASN A 180 111.38 -39.64 REMARK 500 ALA A 210 55.66 36.71 REMARK 500 ASN A 220 56.99 -116.11 REMARK 500 PHE A 264 149.71 -172.80 REMARK 500 ASP A 277 60.47 64.46 REMARK 500 ARG A 302 12.17 -140.60 REMARK 500 PRO A 331 -71.42 -24.87 REMARK 500 ARG A 350 116.45 -36.16 REMARK 500 HIS A 370 -78.81 -56.50 REMARK 500 ILE A 371 83.65 67.92 REMARK 500 VAL A 373 11.95 53.03 REMARK 500 VAL A 400 3.27 -56.13 REMARK 500 GLU A 425 -90.53 -72.18 REMARK 500 PHE A 446 -24.09 -141.92 REMARK 500 ASP A 503 155.78 -29.66 REMARK 500 ASP A 523 60.26 -107.52 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 SF4 A 563 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 441 SG REMARK 620 2 SF4 A 563 S2 114.8 REMARK 620 3 SF4 A 563 S3 116.3 106.8 REMARK 620 4 SF4 A 563 S4 108.2 108.5 101.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 563 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 447 SG REMARK 620 2 SF4 A 563 S1 112.6 REMARK 620 3 SF4 A 563 S2 117.1 106.3 REMARK 620 4 SF4 A 563 S3 109.8 103.5 106.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 563 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 482 SG REMARK 620 2 SF4 A 563 S1 93.1 REMARK 620 3 SF4 A 563 S3 118.2 103.8 REMARK 620 4 SF4 A 563 S4 127.9 107.3 103.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 563 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 486 SG REMARK 620 2 SF4 A 563 S1 123.5 REMARK 620 3 SF4 A 563 S2 111.3 104.7 REMARK 620 4 SF4 A 563 S4 101.0 107.2 108.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SRM A 564 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 486 SG REMARK 620 2 SRM A 564 NA 93.8 REMARK 620 3 SRM A 564 NB 90.6 91.5 REMARK 620 4 SRM A 564 NC 84.6 178.4 88.2 REMARK 620 5 SRM A 564 ND 88.0 89.0 178.5 91.3 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 A 563 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SRM A 564 DBREF 2AKJ A 1 562 UNP P05314 NIR_SPIOL 33 594 SEQADV 2AKJ MET A -45 UNP P05314 EXPRESSION TAG SEQADV 2AKJ HIS A -44 UNP P05314 EXPRESSION TAG SEQADV 2AKJ HIS A -43 UNP P05314 EXPRESSION TAG SEQADV 2AKJ HIS A -42 UNP P05314 EXPRESSION TAG SEQADV 2AKJ HIS A -41 UNP P05314 EXPRESSION TAG SEQADV 2AKJ HIS A -40 UNP P05314 EXPRESSION TAG SEQADV 2AKJ HIS A -39 UNP P05314 EXPRESSION TAG SEQADV 2AKJ SER A -38 UNP P05314 EXPRESSION TAG SEQADV 2AKJ SER A -37 UNP P05314 EXPRESSION TAG SEQADV 2AKJ GLY A -36 UNP P05314 EXPRESSION TAG SEQADV 2AKJ LEU A -35 UNP P05314 EXPRESSION TAG SEQADV 2AKJ VAL A -34 UNP P05314 EXPRESSION TAG SEQADV 2AKJ PRO A -33 UNP P05314 EXPRESSION TAG SEQADV 2AKJ ARG A -32 UNP P05314 EXPRESSION TAG SEQADV 2AKJ GLY A -31 UNP P05314 EXPRESSION TAG SEQADV 2AKJ SER A -30 UNP P05314 EXPRESSION TAG SEQADV 2AKJ GLY A -29 UNP P05314 EXPRESSION TAG SEQADV 2AKJ MET A -28 UNP P05314 EXPRESSION TAG SEQADV 2AKJ LYS A -27 UNP P05314 EXPRESSION TAG SEQADV 2AKJ GLU A -26 UNP P05314 EXPRESSION TAG SEQADV 2AKJ THR A -25 UNP P05314 EXPRESSION TAG SEQADV 2AKJ ALA A -24 UNP P05314 EXPRESSION TAG SEQADV 2AKJ ALA A -23 UNP P05314 EXPRESSION TAG SEQADV 2AKJ ALA A -22 UNP P05314 EXPRESSION TAG SEQADV 2AKJ LYS A -21 UNP P05314 EXPRESSION TAG SEQADV 2AKJ PHE A -20 UNP P05314 EXPRESSION TAG SEQADV 2AKJ GLU A -19 UNP P05314 EXPRESSION TAG SEQADV 2AKJ ARG A -18 UNP P05314 EXPRESSION TAG SEQADV 2AKJ GLN A -17 UNP P05314 EXPRESSION TAG SEQADV 2AKJ HIS A -16 UNP P05314 EXPRESSION TAG SEQADV 2AKJ MET A -15 UNP P05314 EXPRESSION TAG SEQADV 2AKJ ASP A -14 UNP P05314 EXPRESSION TAG SEQADV 2AKJ SER A -13 UNP P05314 EXPRESSION TAG SEQADV 2AKJ PRO A -12 UNP P05314 EXPRESSION TAG SEQADV 2AKJ ASP A -11 UNP P05314 EXPRESSION TAG SEQADV 2AKJ LEU A -10 UNP P05314 EXPRESSION TAG SEQADV 2AKJ GLY A -9 UNP P05314 EXPRESSION TAG SEQADV 2AKJ THR A -8 UNP P05314 EXPRESSION TAG SEQADV 2AKJ ASP A -7 UNP P05314 EXPRESSION TAG SEQADV 2AKJ ASP A -6 UNP P05314 EXPRESSION TAG SEQADV 2AKJ ASP A -5 UNP P05314 EXPRESSION TAG SEQADV 2AKJ ASP A -4 UNP P05314 EXPRESSION TAG SEQADV 2AKJ LYS A -3 UNP P05314 EXPRESSION TAG SEQADV 2AKJ ALA A -2 UNP P05314 EXPRESSION TAG SEQADV 2AKJ MET A -1 UNP P05314 EXPRESSION TAG SEQADV 2AKJ GLY A 0 UNP P05314 EXPRESSION TAG SEQRES 1 A 608 MET HIS HIS HIS HIS HIS HIS SER SER GLY LEU VAL PRO SEQRES 2 A 608 ARG GLY SER GLY MET LYS GLU THR ALA ALA ALA LYS PHE SEQRES 3 A 608 GLU ARG GLN HIS MET ASP SER PRO ASP LEU GLY THR ASP SEQRES 4 A 608 ASP ASP ASP LYS ALA MET GLY CYS GLN LYS ALA VAL SER SEQRES 5 A 608 PRO ALA ALA GLU THR ALA ALA VAL SER PRO SER VAL ASP SEQRES 6 A 608 ALA ALA ARG LEU GLU PRO ARG VAL GLU GLU ARG ASP GLY SEQRES 7 A 608 PHE TRP VAL LEU LYS GLU GLU PHE ARG SER GLY ILE ASN SEQRES 8 A 608 PRO ALA GLU LYS VAL LYS ILE GLU LYS ASP PRO MET LYS SEQRES 9 A 608 LEU PHE ILE GLU ASP GLY ILE SER ASP LEU ALA THR LEU SEQRES 10 A 608 SER MET GLU GLU VAL ASP LYS SER LYS HIS ASN LYS ASP SEQRES 11 A 608 ASP ILE ASP VAL ARG LEU LYS TRP LEU GLY LEU PHE HIS SEQRES 12 A 608 ARG ARG LYS HIS HIS TYR GLY ARG PHE MET MET ARG LEU SEQRES 13 A 608 LYS LEU PRO ASN GLY VAL THR THR SER GLU GLN THR ARG SEQRES 14 A 608 TYR LEU ALA SER VAL ILE LYS LYS TYR GLY LYS ASP GLY SEQRES 15 A 608 CYS ALA ASP VAL THR THR ARG GLN ASN TRP GLN ILE ARG SEQRES 16 A 608 GLY VAL VAL LEU PRO ASP VAL PRO GLU ILE ILE LYS GLY SEQRES 17 A 608 LEU GLU SER VAL GLY LEU THR SER LEU GLN SER GLY MET SEQRES 18 A 608 ASP ASN VAL ARG ASN PRO VAL GLY ASN PRO LEU ALA GLY SEQRES 19 A 608 ILE ASP PRO HIS GLU ILE VAL ASP THR ARG PRO PHE THR SEQRES 20 A 608 ASN LEU ILE SER GLN PHE VAL THR ALA ASN SER ARG GLY SEQRES 21 A 608 ASN LEU SER ILE THR ASN LEU PRO ARG LYS TRP ASN PRO SEQRES 22 A 608 CYS VAL ILE GLY SER HIS ASP LEU TYR GLU HIS PRO HIS SEQRES 23 A 608 ILE ASN ASP LEU ALA TYR MET PRO ALA THR LYS ASN GLY SEQRES 24 A 608 LYS PHE GLY PHE ASN LEU LEU VAL GLY GLY PHE PHE SER SEQRES 25 A 608 ILE LYS ARG CYS GLU GLU ALA ILE PRO LEU ASP ALA TRP SEQRES 26 A 608 VAL SER ALA GLU ASP VAL VAL PRO VAL CYS LYS ALA MET SEQRES 27 A 608 LEU GLU ALA PHE ARG ASP LEU GLY PHE ARG GLY ASN ARG SEQRES 28 A 608 GLN LYS CYS ARG MET MET TRP LEU ILE ASP GLU LEU GLY SEQRES 29 A 608 MET GLU ALA PHE ARG GLY GLU VAL GLU LYS ARG MET PRO SEQRES 30 A 608 GLU GLN VAL LEU GLU ARG ALA SER SER GLU GLU LEU VAL SEQRES 31 A 608 GLN LYS ASP TRP GLU ARG ARG GLU TYR LEU GLY VAL HIS SEQRES 32 A 608 PRO GLN LYS GLN GLN GLY LEU SER PHE VAL GLY LEU HIS SEQRES 33 A 608 ILE PRO VAL GLY ARG LEU GLN ALA ASP GLU MET GLU GLU SEQRES 34 A 608 LEU ALA ARG ILE ALA ASP VAL TYR GLY SER GLY GLU LEU SEQRES 35 A 608 ARG LEU THR VAL GLU GLN ASN ILE ILE ILE PRO ASN VAL SEQRES 36 A 608 GLU ASN SER LYS ILE ASP SER LEU LEU ASN GLU PRO LEU SEQRES 37 A 608 LEU LYS GLU ARG TYR SER PRO GLU PRO PRO ILE LEU MET SEQRES 38 A 608 LYS GLY LEU VAL ALA CYS THR GLY SER GLN PHE CYS GLY SEQRES 39 A 608 GLN ALA ILE ILE GLU THR LYS ALA ARG ALA LEU LYS VAL SEQRES 40 A 608 THR GLU GLU VAL GLN ARG LEU VAL SER VAL THR ARG PRO SEQRES 41 A 608 VAL ARG MET HIS TRP THR GLY CYS PRO ASN SER CYS GLY SEQRES 42 A 608 GLN VAL GLN VAL ALA ASP ILE GLY PHE MET GLY CYS MET SEQRES 43 A 608 THR ARG ASP GLU ASN GLY LYS PRO CYS GLU GLY ALA ASP SEQRES 44 A 608 VAL PHE VAL GLY GLY ARG ILE GLY SER ASP SER HIS LEU SEQRES 45 A 608 GLY ASP ILE TYR LYS LYS ALA VAL PRO CYS LYS ASP LEU SEQRES 46 A 608 VAL PRO VAL VAL ALA GLU ILE LEU ILE ASN GLN PHE GLY SEQRES 47 A 608 ALA VAL PRO ARG GLU ARG GLU GLU ALA GLU HET SF4 A 563 8 HET SRM A 564 63 HETNAM SF4 IRON/SULFUR CLUSTER HETNAM SRM SIROHEME FORMUL 2 SF4 FE4 S4 FORMUL 3 SRM C42 H44 FE N4 O16 FORMUL 4 HOH *6(H2 O) HELIX 1 1 GLU A 38 ARG A 41 5 4 HELIX 2 2 ASN A 45 LYS A 54 1 10 HELIX 3 3 MET A 57 GLU A 62 1 6 HELIX 4 4 ASP A 63 ALA A 69 1 7 HELIX 5 5 SER A 72 ASP A 77 1 6 HELIX 6 6 SER A 79 VAL A 88 1 10 HELIX 7 7 ARG A 89 LEU A 93 5 5 HELIX 8 8 ARG A 98 TYR A 103 1 6 HELIX 9 9 LEU A 112 ASN A 114 5 3 HELIX 10 10 SER A 119 LYS A 131 1 13 HELIX 11 11 TYR A 132 GLY A 136 5 5 HELIX 12 12 VAL A 152 PRO A 154 5 3 HELIX 13 13 ASP A 155 SER A 165 1 11 HELIX 14 14 THR A 197 THR A 209 1 13 HELIX 15 15 ASN A 215 THR A 219 5 5 HELIX 16 16 HIS A 238 ASN A 242 5 5 HELIX 17 17 ASP A 284 GLY A 300 1 17 HELIX 18 18 ASN A 304 CYS A 308 5 5 HELIX 19 19 ARG A 309 GLY A 318 1 10 HELIX 20 20 GLY A 318 LYS A 328 1 11 HELIX 21 21 ILE A 371 VAL A 373 5 3 HELIX 22 22 GLN A 377 GLY A 392 1 16 HELIX 23 23 LYS A 413 LEU A 418 1 6 HELIX 24 24 GLU A 420 GLU A 425 1 6 HELIX 25 25 LEU A 434 LYS A 436 5 3 HELIX 26 26 THR A 442 PHE A 446 5 5 HELIX 27 27 THR A 454 LEU A 468 1 15 HELIX 28 28 GLN A 488 ALA A 492 5 5 HELIX 29 29 ASP A 538 PHE A 551 1 14 SHEET 1 A 2 VAL A 27 ARG A 30 0 SHEET 2 A 2 PHE A 33 LEU A 36 -1 O PHE A 33 N ARG A 30 SHEET 1 B 5 LEU A 95 HIS A 97 0 SHEET 2 B 5 PHE A 106 ARG A 109 -1 O MET A 107 N PHE A 96 SHEET 3 B 5 TRP A 146 VAL A 151 -1 O VAL A 151 N PHE A 106 SHEET 4 B 5 ALA A 138 VAL A 140 -1 N ASP A 139 O GLN A 147 SHEET 5 B 5 ARG A 375 LEU A 376 -1 O LEU A 376 N ALA A 138 SHEET 1 C 5 VAL A 116 THR A 118 0 SHEET 2 C 5 GLU A 395 THR A 399 -1 O LEU A 396 N THR A 117 SHEET 3 C 5 ASN A 403 GLU A 410 -1 O ILE A 405 N ARG A 397 SHEET 4 C 5 LEU A 364 LEU A 369 -1 N VAL A 367 O ILE A 406 SHEET 5 C 5 GLY A 355 PRO A 358 -1 N HIS A 357 O PHE A 366 SHEET 1 D 4 PRO A 227 VAL A 229 0 SHEET 2 D 4 LEU A 244 THR A 250 1 O TYR A 246 N CYS A 228 SHEET 3 D 4 PHE A 255 VAL A 261 -1 O ASN A 258 N MET A 247 SHEET 4 D 4 ILE A 274 SER A 281 -1 O LEU A 276 N LEU A 259 SHEET 1 E 2 PHE A 264 PHE A 265 0 SHEET 2 E 2 CYS A 270 GLU A 271 -1 O GLU A 271 N PHE A 264 SHEET 1 F 5 GLY A 437 ALA A 440 0 SHEET 2 F 5 ARG A 476 THR A 480 1 O TRP A 479 N VAL A 439 SHEET 3 F 5 ILE A 494 ARG A 502 1 O PHE A 496 N THR A 480 SHEET 4 F 5 PRO A 508 VAL A 516 -1 O GLY A 511 N CYS A 499 SHEET 5 F 5 ASP A 528 PRO A 535 -1 O TYR A 530 N VAL A 514 SHEET 1 G 2 VAL A 469 SER A 470 0 SHEET 2 G 2 VAL A 554 PRO A 555 -1 O VAL A 554 N SER A 470 LINK SG CYS A 441 FE1 SF4 A 563 1555 1555 2.32 LINK SG CYS A 447 FE4 SF4 A 563 1555 1555 2.29 LINK SG CYS A 482 FE2 SF4 A 563 1555 1555 2.30 LINK SG CYS A 486 FE3 SF4 A 563 1555 1555 2.31 LINK SG CYS A 486 FE SRM A 564 1555 1555 2.31 SITE 1 AC1 8 CYS A 441 CYS A 447 ALA A 450 THR A 480 SITE 2 AC1 8 GLY A 481 CYS A 482 ASN A 484 CYS A 486 SITE 1 AC2 22 ARG A 98 ARG A 109 THR A 141 THR A 142 SITE 2 AC2 22 ARG A 143 ASN A 145 GLN A 147 ARG A 149 SITE 3 AC2 22 ARG A 223 LYS A 224 ASN A 226 PHE A 264 SITE 4 AC2 22 PHE A 265 SER A 266 GLN A 306 ARG A 309 SITE 5 AC2 22 GLN A 402 CYS A 441 THR A 442 ASN A 484 SITE 6 AC2 22 CYS A 486 GLN A 488 CRYST1 128.970 128.970 120.950 90.00 90.00 90.00 P 41 21 2 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 0.007754 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007754 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008268 0.00000