HEADER OXIDOREDUCTASE 02-FEB-15 4XYD TITLE NITRIC OXIDE REDUCTASE FROM ROSEOBACTER DENITRIFICANS (RDNOR) COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITRIC-OXIDE REDUCTASE SUBUNIT B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NITRIC OXIDE REDUCTASE LARGE SUBUNIT (NORB); COMPND 5 EC: 1.7.2.5; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: NORC-LIKE PROTEIN; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: NITRIC OXIDE REDUCTASE SMALL SUBUNIT (NORC); COMPND 10 EC: 1.7.2.5 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ROSEOBACTER DENITRIFICANS (STRAIN ATCC 33942 / SOURCE 3 OCH 114); SOURCE 4 ORGANISM_COMMON: ERYTHROBACTER SP. (STRAIN OCH 114); SOURCE 5 ORGANISM_TAXID: 375451; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: ROSEOBACTER DENITRIFICANS (STRAIN ATCC 33942 / SOURCE 8 OCH 114); SOURCE 9 ORGANISM_COMMON: ERYTHROBACTER SP. (STRAIN OCH 114); SOURCE 10 ORGANISM_TAXID: 375451 KEYWDS NITRIC OXIDE REDUCTASE, MEMBRANE PROTEIN, HEME COPPER OXIDASE KEYWDS 2 SUPERFAMILY, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR A.CROW REVDAT 4 10-JAN-24 4XYD 1 LINK REVDAT 3 22-JUN-16 4XYD 1 JRNL REVDAT 2 01-JUN-16 4XYD 1 JRNL REVDAT 1 25-MAY-16 4XYD 0 JRNL AUTH A.CROW,Y.MATSUDA,H.ARATA,A.OUBRIE JRNL TITL STRUCTURE OF THE MEMBRANE-INTRINSIC NITRIC OXIDE REDUCTASE JRNL TITL 2 FROM ROSEOBACTER DENITRIFICANS. JRNL REF BIOCHEMISTRY V. 55 3198 2016 JRNL REFN ISSN 0006-2960 JRNL PMID 27185533 JRNL DOI 10.1021/ACS.BIOCHEM.6B00332 REMARK 2 REMARK 2 RESOLUTION. 2.85 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) : 2.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 23917 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1285 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) : 2.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.92 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1428 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.07 REMARK 3 BIN R VALUE (WORKING SET) : 0.3070 REMARK 3 BIN FREE R VALUE SET COUNT : 79 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4706 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 134 REMARK 3 SOLVENT ATOMS : 16 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.45000 REMARK 3 B22 (A**2) : -5.43000 REMARK 3 B33 (A**2) : 6.88000 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): 0.580 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.322 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.254 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.740 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.875 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5050 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6898 ; 1.588 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 592 ; 5.421 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 208 ;36.768 ;22.885 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 750 ;19.465 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;17.190 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 735 ; 0.109 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3822 ; 0.006 ; 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): 2369 ; 3.108 ; 5.671 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2960 ; 4.981 ; 8.505 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2680 ; 3.507 ; 5.821 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): 8647 ; 7.815 ;49.825 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 : 1.40 REMARK 3 ION PROBE RADIUS : 0.85 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 4XYD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000206519. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25236 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850 REMARK 200 RESOLUTION RANGE LOW (A) : 53.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10200 REMARK 200 FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.36200 REMARK 200 FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3O0R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION REAGENT COMPOSED OF REMARK 280 100 MM MOPS PH 7.6, 28 % (W/V) PEG 600. PROTEIN SOLUTION 8MG/ML REMARK 280 20 MM MOPS PH 7.2, 100 MM NACL, 0.4 % (W/V) NONYL-B-D- REMARK 280 GLUCOPYRANOSIDE. MIXED 1:1 IN SITTING DROP AT 4C., VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.41500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.39000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.41500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 63.39000 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: 10530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -146.0 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 SER A 446 REMARK 465 PRO A 447 REMARK 465 SER A 448 REMARK 465 ASP A 449 REMARK 465 LYS A 450 REMARK 465 GLN A 451 REMARK 465 PRO A 452 REMARK 465 VAL A 453 REMARK 465 ALA A 454 REMARK 465 ALA A 455 REMARK 465 GLU A 456 REMARK 465 MET B 1 REMARK 465 ARG B 2 REMARK 465 ASP B 3 REMARK 465 VAL B 4 REMARK 465 LEU B 5 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 ND1 HIS A 194 OE1 GLU A 198 2.12 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 168 CA - CB - CG ANGL. DEV. = 13.9 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 LEU A 40 26.77 48.18 REMARK 500 GLU A 78 29.57 49.35 REMARK 500 PHE A 123 -2.45 68.14 REMARK 500 TRP A 196 -76.59 -78.00 REMARK 500 ARG A 221 -59.20 -16.43 REMARK 500 LYS A 360 71.96 35.98 REMARK 500 LEU B 46 65.88 -68.72 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 HEM A 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 53 NE2 REMARK 620 2 HEM A 501 NA 93.4 REMARK 620 3 HEM A 501 NB 90.7 90.1 REMARK 620 4 HEM A 501 NC 85.7 178.5 88.6 REMARK 620 5 HEM A 501 ND 89.7 90.1 179.6 91.1 REMARK 620 6 HIS A 336 NE2 169.4 97.0 91.0 83.9 88.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 503 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 122 OE1 REMARK 620 2 GLU A 122 OE2 45.1 REMARK 620 3 HEM A 501 O1D 108.7 67.1 REMARK 620 4 HEM A 504 O1A 80.0 84.6 73.3 REMARK 620 5 HEM A 504 O2A 81.7 114.1 114.2 43.8 REMARK 620 6 GLY B 72 O 80.7 79.3 109.7 160.4 135.9 REMARK 620 7 TYR B 74 OH 158.9 153.7 92.4 106.0 88.9 93.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 505 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 194 ND1 REMARK 620 2 GLU A 198 OE1 65.3 REMARK 620 3 GLU A 198 OE2 96.0 54.4 REMARK 620 4 HIS A 245 NE2 106.4 137.8 87.8 REMARK 620 5 HIS A 246 NE2 96.5 130.4 167.3 90.7 REMARK 620 6 UNL A 502 O2 142.8 79.4 70.8 107.6 97.7 REMARK 620 7 UNL A 502 O1 117.7 67.7 87.9 135.9 84.5 31.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 504 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 334 NE2 REMARK 620 2 HEM A 504 NA 96.3 REMARK 620 3 HEM A 504 NB 93.7 88.8 REMARK 620 4 HEM A 504 NC 83.4 178.1 89.4 REMARK 620 5 HEM A 504 ND 85.2 91.7 178.8 90.2 REMARK 620 6 UNL A 502 O2 160.8 98.1 99.2 82.6 81.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU B 202 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 49 OE1 REMARK 620 2 HIS B 52 ND1 106.9 REMARK 620 3 GLU B 124 OE1 105.9 99.4 REMARK 620 4 HOH B 304 O 118.4 104.5 119.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC B 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 66 NE2 REMARK 620 2 HEC B 201 NA 92.3 REMARK 620 3 HEC B 201 NB 88.7 89.8 REMARK 620 4 HEC B 201 NC 87.6 179.8 90.1 REMARK 620 5 HEC B 201 ND 91.3 90.3 179.9 89.9 REMARK 620 6 MET B 116 SD 176.6 89.2 94.4 90.9 85.6 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEC B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU B 202 DBREF 4XYD A 1 456 UNP Q16A04 Q16A04_ROSDO 1 456 DBREF 4XYD B 1 150 UNP Q16A03 Q16A03_ROSDO 1 150 SEQRES 1 A 456 MET LYS TYR GLN SER GLN SER ILE ALA LEU VAL TYR PHE SEQRES 2 A 456 ALA VAL ALA LEU GLY LEU PHE ALA ILE GLN VAL SER GLY SEQRES 3 A 456 GLY LEU LEU LEU GLY TRP ILE TYR VAL SER PRO ASN PHE SEQRES 4 A 456 LEU SER GLU ILE LEU PRO PHE ASN ILE VAL ARG MET LEU SEQRES 5 A 456 HIS THR ASN SER LEU ILE VAL TRP LEU LEU LEU GLY PHE SEQRES 6 A 456 MET GLY ALA ALA TYR PHE VAL ILE PRO GLU GLU SER GLU SEQRES 7 A 456 ARG GLU ILE HIS SER PRO LEU LEU ALA TYR LEU GLN LEU SEQRES 8 A 456 ALA ILE MET VAL LEU GLY THR LEU GLY VAL VAL VAL THR SEQRES 9 A 456 TYR LEU PHE ASN LEU PHE GLU GLY ASN TRP LEU LEU GLY SEQRES 10 A 456 LYS GLU GLY ARG GLU PHE LEU GLU GLN PRO VAL TRP VAL SEQRES 11 A 456 LYS MET GLY ILE VAL VAL ALA ALA LEU ILE PHE MET TYR SEQRES 12 A 456 ASN ILE SER MET THR VAL LEU GLN GLY ARG LYS THR ALA SEQRES 13 A 456 ILE THR ASN VAL LEU LEU LEU GLY LEU TRP GLY LEU THR SEQRES 14 A 456 LEU LEU PHE LEU PHE ALA PHE TYR ASN PRO SER ASN LEU SEQRES 15 A 456 ALA LEU ASP LYS MET TYR TRP TRP TYR VAL VAL HIS LEU SEQRES 16 A 456 TRP VAL GLU GLY THR TRP GLU LEU VAL MET ALA SER VAL SEQRES 17 A 456 LEU ALA PHE LEU MET LEU LYS LEU THR GLY VAL ASP ARG SEQRES 18 A 456 GLU ILE ILE GLU LYS TRP LEU TYR LEU ILE VAL ALA THR SEQRES 19 A 456 ALA LEU PHE SER GLY ILE LEU GLY THR GLY HIS HIS TYR SEQRES 20 A 456 PHE TRP ILE GLY THR PRO GLY TYR TRP GLN TRP ILE GLY SEQRES 21 A 456 SER ILE PHE SER ALA LEU GLU VAL VAL PRO PHE PHE GLY SEQRES 22 A 456 MET MET ALA PHE ALA PHE VAL MET VAL TRP LYS GLY ARG SEQRES 23 A 456 LYS ASP HIS PRO ASN LYS ALA ALA LEU LEU TRP SER LEU SEQRES 24 A 456 GLY CYS ALA THR LEU ALA PHE PHE GLY ALA GLY VAL TRP SEQRES 25 A 456 GLY PHE LEU HIS THR LEU HIS GLY ILE ASN TYR TYR THR SEQRES 26 A 456 HIS GLY THR GLN ILE THR ALA ALA HIS GLY HIS LEU ALA SEQRES 27 A 456 PHE PHE GLY ALA TYR VAL SER LEU ASN LEU ALA ILE PHE SEQRES 28 A 456 SER TYR ALA PHE PRO ILE LEU ARG LYS ARG ASP PRO TYR SEQRES 29 A 456 ASN GLN VAL LEU ASN MET ALA SER PHE TRP LEU MET ALA SEQRES 30 A 456 GLY GLY MET THR PHE MET THR PHE VAL LEU THR PHE ALA SEQRES 31 A 456 GLY THR VAL GLN THR HIS ALA GLN ARG VAL GLN GLY ASP SEQRES 32 A 456 TYR PHE MET ASP VAL GLN ASP ALA ILE THR ILE PHE TYR SEQRES 33 A 456 TRP MET ARG PHE GLY SER GLY ILE ALA VAL VAL LEU GLY SEQRES 34 A 456 ALA LEU LEU PHE ILE TYR ALA VAL ALA VAL PRO ARG LYS SEQRES 35 A 456 GLU ILE ILE SER PRO SER ASP LYS GLN PRO VAL ALA ALA SEQRES 36 A 456 GLU SEQRES 1 B 150 MET ARG ASP VAL LEU THR THR SER MET ALA ARG ASN ILE SEQRES 2 B 150 PHE TYR GLY GLY SER LEU PHE PHE ILE LEU ILE PHE VAL SEQRES 3 B 150 GLY LEU SER VAL HIS SER HIS ARG TYR ILE VAL THR THR SEQRES 4 B 150 SER THR ASP ALA ALA THR LEU THR ALA GLU VAL GLU HIS SEQRES 5 B 150 GLY LYS HIS LEU TRP GLU ILE HIS GLY CYS VAL ASN CYS SEQRES 6 B 150 HIS SER ILE LEU GLY GLU GLY ALA TYR PHE ALA PRO GLU SEQRES 7 B 150 LEU GLY ASN VAL MET THR ARG TRP GLY VAL GLU ASP ASP SEQRES 8 B 150 PRO ASP ALA ALA PHE GLU ALA LEU LYS GLY TRP MET ASP SEQRES 9 B 150 ALA MET PRO THR GLY ILE GLU GLY ARG ARG GLN MET PRO SEQRES 10 B 150 ASN PHE GLY LEU ASN ASP GLU GLU TYR ARG ALA LEU SER SEQRES 11 B 150 ASP PHE LEU LEU TRP THR ASN THR ILE ARG ASN GLN ASP SEQRES 12 B 150 TRP PRO PRO ASN ASP ALA GLY HET HEM A 501 43 HET UNL A 502 2 HET CA A 503 1 HET HEM A 504 43 HET FE A 505 1 HET HEC B 201 43 HET CU B 202 1 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM UNL UNKNOWN LIGAND HETNAM CA CALCIUM ION HETNAM FE FE (III) ION HETNAM HEC HEME C HETNAM CU COPPER (II) ION HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 5 CA CA 2+ FORMUL 7 FE FE 3+ FORMUL 8 HEC C34 H34 FE N4 O4 FORMUL 9 CU CU 2+ FORMUL 10 HOH *16(H2 O) HELIX 1 AA1 TYR A 3 GLN A 6 5 4 HELIX 2 AA2 SER A 7 SER A 36 1 30 HELIX 3 AA3 PRO A 45 GLU A 78 1 34 HELIX 4 AA4 SER A 83 ASN A 108 1 26 HELIX 5 AA5 PRO A 127 GLN A 151 1 25 HELIX 6 AA6 THR A 155 LEU A 173 1 19 HELIX 7 AA7 PHE A 174 TYR A 177 5 4 HELIX 8 AA8 ASN A 181 GLU A 198 1 18 HELIX 9 AA9 GLY A 199 GLY A 218 1 20 HELIX 10 AB1 ASP A 220 GLY A 242 1 23 HELIX 11 AB2 THR A 243 TYR A 247 5 5 HELIX 12 AB3 TYR A 255 LEU A 266 1 12 HELIX 13 AB4 GLU A 267 GLY A 285 1 19 HELIX 14 AB5 ASN A 291 ALA A 309 1 19 HELIX 15 AB6 GLY A 310 HIS A 316 1 7 HELIX 16 AB7 LEU A 318 HIS A 326 1 9 HELIX 17 AB8 THR A 328 TYR A 343 1 16 HELIX 18 AB9 TYR A 343 ARG A 359 1 17 HELIX 19 AC1 ASN A 365 VAL A 400 1 36 HELIX 20 AC2 TYR A 404 ILE A 412 1 9 HELIX 21 AC3 ILE A 412 VAL A 439 1 28 HELIX 22 AC4 THR B 7 THR B 39 1 33 HELIX 23 AC5 THR B 47 GLY B 61 1 15 HELIX 24 AC6 CYS B 62 CYS B 65 5 4 HELIX 25 AC7 ASN B 81 TRP B 86 1 6 HELIX 26 AC8 ASP B 91 MET B 106 1 16 HELIX 27 AC9 ASN B 122 THR B 138 1 17 SHEET 1 AA1 2 SER B 67 ILE B 68 0 SHEET 2 AA1 2 GLU B 71 GLY B 72 -1 O GLU B 71 N ILE B 68 LINK SG CYS B 62 CAB HEC B 201 1555 1555 1.66 LINK SG CYS B 65 CAC HEC B 201 1555 1555 1.72 LINK NE2 HIS A 53 FE HEM A 501 1555 1555 1.91 LINK OE1 GLU A 122 CA CA A 503 1555 1555 2.35 LINK OE2 GLU A 122 CA CA A 503 1555 1555 3.07 LINK ND1 HIS A 194 FE FE A 505 1555 1555 1.89 LINK OE1 GLU A 198 FE FE A 505 1555 1555 2.03 LINK OE2 GLU A 198 FE FE A 505 1555 1555 2.63 LINK NE2 HIS A 245 FE FE A 505 1555 1555 1.90 LINK NE2 HIS A 246 FE FE A 505 1555 1555 1.91 LINK NE2 HIS A 334 FE HEM A 504 1555 1555 1.95 LINK NE2 HIS A 336 FE HEM A 501 1555 1555 1.85 LINK O1D HEM A 501 CA CA A 503 1555 1555 2.33 LINK O2 UNL A 502 FE HEM A 504 1555 1555 2.01 LINK O2 UNL A 502 FE FE A 505 1555 1555 2.32 LINK O1 UNL A 502 FE FE A 505 1555 1555 2.06 LINK CA CA A 503 O1A HEM A 504 1555 1555 2.33 LINK CA CA A 503 O2A HEM A 504 1555 1555 3.14 LINK CA CA A 503 O GLY B 72 1555 1555 2.32 LINK CA CA A 503 OH TYR B 74 1555 1555 2.36 LINK OE1AGLU B 49 CU CU B 202 1555 1555 1.92 LINK ND1 HIS B 52 CU CU B 202 1555 1555 2.03 LINK NE2 HIS B 66 FE HEC B 201 1555 1555 1.88 LINK SD MET B 116 FE HEC B 201 1555 1555 2.25 LINK OE1 GLU B 124 CU CU B 202 1555 1555 1.92 LINK CU CU B 202 O HOH B 304 1555 1555 1.94 CISPEP 1 MET B 106 PRO B 107 0 -1.47 CISPEP 2 TRP B 144 PRO B 145 0 -0.61 SITE 1 AC1 20 GLN A 23 VAL A 24 GLY A 27 LEU A 28 SITE 2 AC1 20 LEU A 30 TYR A 34 ARG A 50 HIS A 53 SITE 3 AC1 20 LEU A 57 GLU A 122 HIS A 336 PHE A 339 SITE 4 AC1 20 VAL A 344 MET A 380 ARG A 419 VAL A 427 SITE 5 AC1 20 CA A 503 HEM A 504 ALA B 73 TYR B 74 SITE 1 AC2 5 GLU A 122 HEM A 501 HEM A 504 GLY B 72 SITE 2 AC2 5 TYR B 74 SITE 1 AC3 25 GLU A 122 PHE A 123 TRP A 190 VAL A 197 SITE 2 AC3 25 GLU A 198 HIS A 245 HIS A 246 GLU A 267 SITE 3 AC3 25 PHE A 271 ALA A 309 GLY A 313 PHE A 314 SITE 4 AC3 25 HIS A 316 THR A 317 ASN A 322 HIS A 326 SITE 5 AC3 25 GLY A 327 THR A 331 HIS A 334 ALA A 338 SITE 6 AC3 25 PHE A 339 TYR A 343 HEM A 501 CA A 503 SITE 7 AC3 25 HOH A 609 SITE 1 AC4 4 HIS A 194 GLU A 198 HIS A 245 HIS A 246 SITE 1 AC5 19 ASN A 47 MET A 406 GLY B 61 CYS B 62 SITE 2 AC5 19 CYS B 65 HIS B 66 ALA B 76 PRO B 77 SITE 3 AC5 19 LEU B 79 ARG B 85 TRP B 86 LEU B 99 SITE 4 AC5 19 TRP B 102 ARG B 113 ARG B 114 GLN B 115 SITE 5 AC5 19 MET B 116 PRO B 117 HOH B 303 SITE 1 AC6 4 GLU B 49 HIS B 52 GLU B 124 HOH B 304 CRYST1 86.220 98.830 126.780 90.00 90.00 90.00 P 2 21 21 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 0.011598 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010118 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007888 0.00000