HEADER OXIDOREDUCTASE 11-SEP-15 5DOQ TITLE THE STRUCTURE OF BD OXIDASE FROM GEOBACILLUS THERMODENITRIFICANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: BD-TYPE QUINOL OXIDASE SUBUNIT I; COMPND 3 CHAIN: A; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: BD-TYPE QUINOL OXIDASE SUBUNIT II; COMPND 6 CHAIN: B; COMPND 7 MOL_ID: 3; COMPND 8 MOLECULE: PUTATIVE MEMBRANE PROTEIN; COMPND 9 CHAIN: C SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS THERMODENITRIFICANS (STRAIN NG80- SOURCE 3 2); SOURCE 4 ORGANISM_TAXID: 420246; SOURCE 5 STRAIN: NG80-2; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: GEOBACILLUS THERMODENITRIFICANS (STRAIN NG80- SOURCE 8 2); SOURCE 9 ORGANISM_TAXID: 420246; SOURCE 10 STRAIN: NG80-2; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: GEOBACILLUS SP. PA-3; SOURCE 13 ORGANISM_TAXID: 1699078 KEYWDS BD OXIDASE, TERMINAL OXIDASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.SAFARIAN,H.MUELLER,C.RAJENDRAN,J.PREU,S.OVCHINNIKOV,T.KUSUMOTO, AUTHOR 2 T.HIROSE,J.LANGER,J.SAKAMOTO,H.MICHEL REVDAT 3 08-MAY-24 5DOQ 1 REMARK REVDAT 2 18-APR-18 5DOQ 1 JRNL REVDAT 1 04-MAY-16 5DOQ 0 JRNL AUTH S.SAFARIAN,C.RAJENDRAN,H.MULLER,J.PREU,J.D.LANGER, JRNL AUTH 2 S.OVCHINNIKOV,T.HIROSE,T.KUSUMOTO,J.SAKAMOTO,H.MICHEL JRNL TITL STRUCTURE OF A BD OXIDASE INDICATES SIMILAR MECHANISMS FOR JRNL TITL 2 MEMBRANE-INTEGRATED OXYGEN REDUCTASES. JRNL REF SCIENCE V. 352 583 2016 JRNL REFN ESSN 1095-9203 JRNL PMID 27126043 JRNL DOI 10.1126/SCIENCE.AAF2477 REMARK 2 REMARK 2 RESOLUTION. 3.05 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) : 3.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 57.0 REMARK 3 NUMBER OF REFLECTIONS : 17360 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) : 0.320 REMARK 3 R VALUE (WORKING SET) : 0.319 REMARK 3 FREE R VALUE : 0.335 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 897 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) : 3.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.12 REMARK 3 REFLECTION IN BIN (WORKING SET) : 66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 2.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.6140 REMARK 3 BIN FREE R VALUE SET COUNT : 1 REMARK 3 BIN FREE R VALUE : 1.1820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6341 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 130 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 120.3 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.15000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : 0.17000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.763 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.588 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 36.631 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.879 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.873 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6693 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6517 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9191 ; 1.112 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14681 ; 0.733 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 789 ; 6.130 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 261 ;34.822 ;22.299 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1004 ;12.088 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;10.966 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1025 ; 0.053 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7382 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1623 ; 0.001 ; 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): 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 5DOQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000213561. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.738290 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18373 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.050 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 56.7 REMARK 200 DATA REDUNDANCY : 31.44 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : 0.09700 REMARK 200 FOR THE DATA SET : 19.1700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 2.6 REMARK 200 DATA REDUNDANCY IN SHELL : 19.15 REMARK 200 R MERGE FOR SHELL (I) : 2.20000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.030 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX, PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 400, AMMONIUM SULFATE, NA-HEPES, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 55.03000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.36000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 60.43000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.36000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 55.03000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 60.43000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -146.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 VAL A 433 REMARK 465 GLU A 434 REMARK 465 ARG A 435 REMARK 465 GLU A 436 REMARK 465 LEU A 437 REMARK 465 GLU A 438 REMARK 465 GLU A 439 REMARK 465 ARG A 440 REMARK 465 ALA A 441 REMARK 465 ASN A 442 REMARK 465 ARG A 443 REMARK 465 GLY A 444 REMARK 465 GLU A 445 REMARK 465 VAL A 446 REMARK 465 ALA A 447 REMARK 465 PRO A 448 REMARK 465 ALA B 331 REMARK 465 TYR B 332 REMARK 465 VAL B 333 REMARK 465 LYS B 334 REMARK 465 GLY B 335 REMARK 465 LYS B 336 REMARK 465 TRP B 337 REMARK 465 GLU B 338 REMARK 465 GLY B 339 REMARK 465 GLY B 340 REMARK 465 LYS B 341 REMARK 465 GLY B 342 REMARK 465 MET C 763 REMARK 465 GLN C 764 REMARK 465 THR C 765 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 TYR A 4 -36.16 -136.17 REMARK 500 ALA A 25 -59.54 -133.38 REMARK 500 MET A 48 42.79 -86.81 REMARK 500 LEU A 79 -77.55 -39.95 REMARK 500 LEU A 89 -62.80 -96.32 REMARK 500 ARG A 121 -63.23 -149.31 REMARK 500 ASN A 124 145.74 68.85 REMARK 500 PRO A 156 177.20 -51.25 REMARK 500 GLN A 157 -123.89 -129.88 REMARK 500 ASN A 163 49.72 38.20 REMARK 500 PHE A 176 49.95 -94.07 REMARK 500 SER A 191 -34.60 -172.78 REMARK 500 LYS A 209 -101.06 -77.38 REMARK 500 ASN A 211 70.33 -60.13 REMARK 500 ILE A 214 -92.31 -12.01 REMARK 500 HIS A 259 73.62 -102.26 REMARK 500 SER A 264 -70.33 -75.83 REMARK 500 GLU A 276 -33.83 -28.82 REMARK 500 ASP A 277 59.14 -105.52 REMARK 500 ASN A 278 77.92 49.35 REMARK 500 LYS A 281 -104.56 -102.70 REMARK 500 ALA A 289 -65.62 -98.46 REMARK 500 LEU A 290 62.40 -69.07 REMARK 500 SER A 291 -47.78 -169.74 REMARK 500 TYR A 339 -70.07 -36.28 REMARK 500 LEU A 341 -78.19 -66.64 REMARK 500 ILE A 344 -61.63 -125.81 REMARK 500 ARG A 346 -91.73 -139.47 REMARK 500 LYS A 348 62.06 24.59 REMARK 500 LEU A 386 1.29 -68.60 REMARK 500 ARG A 387 -86.13 -121.40 REMARK 500 TYR A 389 -99.89 -96.88 REMARK 500 GLU A 394 44.03 -103.83 REMARK 500 THR A 397 -81.94 -122.55 REMARK 500 SER A 399 -62.85 -99.15 REMARK 500 PHE B 30 -68.78 -178.38 REMARK 500 ASN B 39 81.90 62.61 REMARK 500 TYR B 80 -74.93 -68.34 REMARK 500 ARG B 113 -38.82 -36.31 REMARK 500 GLU B 145 -150.57 -110.61 REMARK 500 ASN B 146 -89.18 -82.52 REMARK 500 ALA B 148 34.83 -159.89 REMARK 500 SER B 170 -79.12 -89.27 REMARK 500 PRO B 208 -43.03 -26.29 REMARK 500 HIS B 223 -79.20 -97.16 REMARK 500 ARG B 254 -100.39 -106.68 REMARK 500 GLN B 268 -74.52 -52.51 REMARK 500 LEU B 285 -67.63 76.97 REMARK 500 LYS C 789 -73.92 -71.42 REMARK 500 ASP C 790 49.81 -108.93 REMARK 500 REMARK 500 THIS ENTRY HAS 51 RAMACHANDRAN OUTLIERS. 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 HEB A 502 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 21 NE2 REMARK 620 2 HEB A 502 NA 102.3 REMARK 620 3 HEB A 502 NB 91.8 93.1 REMARK 620 4 HEB A 502 NC 78.7 173.9 92.9 REMARK 620 5 HEB A 502 ND 88.7 90.5 176.2 83.5 REMARK 620 6 GLU A 101 OE2 165.4 90.4 80.3 89.4 98.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEB A 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 186 NE2 REMARK 620 2 HEB A 501 NA 103.4 REMARK 620 3 HEB A 501 NB 107.3 91.6 REMARK 620 4 HEB A 501 NC 75.2 173.9 94.5 REMARK 620 5 HEB A 501 ND 72.7 91.3 177.1 82.6 REMARK 620 6 MET A 325 SD 153.8 102.7 74.9 78.6 103.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HDD A 503 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 378 OE2 REMARK 620 2 HDD A 503 NA 62.2 REMARK 620 3 HDD A 503 NB 72.1 88.7 REMARK 620 4 HDD A 503 NC 107.7 169.9 87.5 REMARK 620 5 HDD A 503 ND 101.1 92.6 171.5 89.8 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 HEB A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEB A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HDD A 503 DBREF 5DOQ A 1 448 UNP A4IKP6 A4IKP6_GEOTN 1 448 DBREF 5DOQ B 1 342 UNP A4IKP7 A4IKP7_GEOTN 1 342 DBREF1 5DOQ C 763 795 UNP A0A0Q0UXS2_9BACI DBREF2 5DOQ C A0A0Q0UXS2 1 33 SEQADV 5DOQ GLU A 123 UNP A4IKP6 LYS 123 CONFLICT SEQADV 5DOQ ASN B 146 UNP A4IKP7 SER 146 CONFLICT SEQRES 1 A 448 MET ASN GLY TYR ASP PRO VAL LEU LEU SER ARG ILE LEU SEQRES 2 A 448 THR GLU LEU THR LEU THR VAL HIS ILE ILE TYR ALA THR SEQRES 3 A 448 ILE GLY VAL GLY VAL PRO LEU MET ILE ALA ILE ALA GLN SEQRES 4 A 448 TRP VAL GLY ILE ARG LYS ASN ASP MET HIS TYR ILE LEU SEQRES 5 A 448 LEU ALA ARG ARG TRP THR ARG GLY PHE VAL ILE THR VAL SEQRES 6 A 448 ALA VAL GLY VAL VAL THR GLY THR ALA ILE GLY LEU GLN SEQRES 7 A 448 LEU SER LEU LEU TRP PRO ASN PHE MET GLN LEU ALA GLY SEQRES 8 A 448 GLN VAL ILE SER LEU PRO LEU PHE MET GLU THR PHE ALA SEQRES 9 A 448 PHE PHE PHE GLU ALA ILE PHE LEU GLY ILE TYR LEU TYR SEQRES 10 A 448 THR TRP ASP ARG PHE GLU ASN GLN LYS LYS HIS LEU LEU SEQRES 11 A 448 LEU LEU ILE PRO VAL ALA ILE GLY SER SER ALA SER ALA SEQRES 12 A 448 MET PHE ILE THR MET VAL ASN ALA PHE MET ASN THR PRO SEQRES 13 A 448 GLN GLY PHE GLU LEU LYS ASN GLY GLU LEU VAL ASN ILE SEQRES 14 A 448 ASP PRO ILE VAL ALA MET PHE ASN PRO ALA MET PRO THR SEQRES 15 A 448 LYS VAL ALA HIS VAL LEU ALA THR SER TYR MET THR SER SEQRES 16 A 448 ALA PHE VAL LEU ALA SER ILE ALA ALA TRP HIS LEU TRP SEQRES 17 A 448 LYS GLY ASN ARG HIS ILE TYR HIS ARG LYS ALA LEU HIS SEQRES 18 A 448 LEU THR MET LYS THR ALA PHE ILE PHE SER VAL ALA SER SEQRES 19 A 448 ALA LEU VAL GLY ASP LEU SER GLY LYS PHE LEU ALA GLU SEQRES 20 A 448 TYR GLN PRO GLU LYS LEU ALA ALA ALA GLU TRP HIS PHE SEQRES 21 A 448 GLU THR SER SER HIS ALA PRO LEU ILE LEU PHE GLY THR SEQRES 22 A 448 LEU GLU GLU ASP ASN GLU VAL LYS TYR ALA LEU GLU ILE SEQRES 23 A 448 PRO TYR ALA LEU SER ILE LEU ALA HIS ASN HIS PRO ALA SEQRES 24 A 448 ALA VAL VAL THR GLY LEU ASN ASP ILE PRO GLU ASP GLU SEQRES 25 A 448 ARG PRO PRO LEU TYR ILE HIS TYR LEU PHE ASP VAL MET SEQRES 26 A 448 VAL THR ILE GLY VAL PHE LEU MET VAL VAL ALA ALA VAL SEQRES 27 A 448 TYR TRP LEU GLY SER ILE PHE ARG TRP LYS TRP THR ALA SEQRES 28 A 448 LYS ASN TRP PHE PHE GLY LEU LEU VAL ALA GLY GLY PRO SEQRES 29 A 448 LEU ALA MET ILE ALA ILE GLU ALA GLY TRP TYR LEU ALA SEQRES 30 A 448 GLU VAL GLY ARG GLN PRO TRP ILE LEU ARG GLY TYR MET SEQRES 31 A 448 LYS THR ALA GLU GLY ALA THR THR SER ALA HIS VAL ASP SEQRES 32 A 448 THR MET LEU VAL LEU PHE CYS LEU LEU TYR ILE VAL LEU SEQRES 33 A 448 VAL ILE ALA SER ALA THR VAL LEU ILE ARG MET PHE ARG SEQRES 34 A 448 ARG ASN PRO VAL GLU ARG GLU LEU GLU GLU ARG ALA ASN SEQRES 35 A 448 ARG GLY GLU VAL ALA PRO SEQRES 1 B 342 MET THR LEU GLU VAL ILE GLY ILE SER VAL LEU TRP LEU SEQRES 2 B 342 PHE LEU PHE GLY TYR ILE ILE VAL ALA SER ILE ASP PHE SEQRES 3 B 342 GLY ALA GLY PHE PHE SER VAL TYR SER HIS TRP ALA ASN SEQRES 4 B 342 GLN GLN HIS ILE LEU HIS ARG ILE ILE GLN ARG TYR LEU SEQRES 5 B 342 SER PRO VAL TRP GLU VAL THR ASN VAL PHE LEU VAL PHE SEQRES 6 B 342 PHE PHE VAL GLY ILE VAL GLY PHE PHE PRO LYS THR ALA SEQRES 7 B 342 TYR TYR TYR GLY SER ILE LEU LEU VAL PRO ALA SER ILE SEQRES 8 B 342 ALA ILE VAL LEU LEU ALA ILE ARG GLY SER TYR TYR ALA SEQRES 9 B 342 PHE HIS THR TYR GLY GLU THR GLU ARG ASN TRP TYR LEU SEQRES 10 B 342 LEU ALA TYR GLY LEU THR GLY LEU PHE ILE PRO ALA SER SEQRES 11 B 342 LEU SER ILE VAL LEU THR ILE SER GLU GLY GLY PHE VAL SEQRES 12 B 342 GLU GLU ASN ALA ALA GLY VAL ALA LEU ASP TYR GLY LYS SEQRES 13 B 342 LEU PHE ALA SER PRO LEU SER TRP SER VAL VAL LEU LEU SEQRES 14 B 342 SER VAL THR SER VAL LEU TYR ILE SER ALA VAL PHE LEU SEQRES 15 B 342 THR TYR TYR ALA ASP ALA ALA GLY ASP GLU GLN ALA ARG SEQRES 16 B 342 ALA LEU LEU ARG ARG TYR ALA LEU LEU TRP SER GLY PRO SEQRES 17 B 342 THR MET LEU SER ALA LEU LEU ILE ILE TYR GLN LEU ARG SEQRES 18 B 342 TYR HIS ASN PRO GLU HIS TYR ASP ASN LEU TRP ASN VAL SEQRES 19 B 342 ALA TRP MET LEU VAL ILE SER PHE LEU PHE PHE VAL ILE SEQRES 20 B 342 THR VAL TRP LEU LEU GLY ARG GLN ARG ARG PHE GLY TRP SEQRES 21 B 342 ALA PHE ILE ALA LEU LEU PHE GLN TYR ALA PHE ALA PHE SEQRES 22 B 342 TYR ALA TYR GLY ILE SER HIS TYR PRO TYR LEU LEU TYR SEQRES 23 B 342 PRO TYR LEU THR ILE TYR ASP GLY PHE THR ASN GLU THR SEQRES 24 B 342 MET ALA MET ALA LEU ILE VAL ALA PHE ILE ALA GLY LEU SEQRES 25 B 342 LEU LEU LEU ILE PRO SER LEU TYR LEU LEU MET ARG LEU SEQRES 26 B 342 PHE LEU PHE ASN LYS ALA TYR VAL LYS GLY LYS TRP GLU SEQRES 27 B 342 GLY GLY LYS GLY SEQRES 1 C 33 MET GLN THR PHE LEU ILE MET TYR ALA PRO MET VAL VAL SEQRES 2 C 33 VAL ALA LEU SER VAL VAL ALA ALA PHE TRP VAL GLY LEU SEQRES 3 C 33 LYS ASP VAL HIS VAL ASN GLU HET HEB A 501 43 HET HEB A 502 43 HET HDD A 503 44 HETNAM HEB HEME B/C HETNAM HDD CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE HETSYN HEB HYBRID BETWEEN B AND C TYPE HEMES (PROTOPORPHYRIN IX HETSYN 2 HEB CONTAINING FE) HETSYN HDD HEME FORMUL 4 HEB 2(C34 H34 FE N4 O4) FORMUL 6 HDD C34 H32 FE N4 O5 HELIX 1 AA1 TYR A 4 TYR A 24 1 21 HELIX 2 AA2 ALA A 25 ASN A 46 1 22 HELIX 3 AA3 HIS A 49 TRP A 83 1 35 HELIX 4 AA4 TRP A 83 TRP A 119 1 37 HELIX 5 AA5 GLN A 125 THR A 155 1 31 HELIX 6 AA6 ASP A 170 PHE A 176 1 7 HELIX 7 AA7 ALA A 179 LYS A 209 1 31 HELIX 8 AA8 ARG A 212 GLN A 249 1 38 HELIX 9 AA9 GLN A 249 GLU A 257 1 9 HELIX 10 AB1 TYR A 317 SER A 343 1 27 HELIX 11 AB2 LYS A 352 GLY A 380 1 29 HELIX 12 AB3 ARG A 381 LEU A 386 1 6 HELIX 13 AB4 LYS A 391 GLY A 395 5 5 HELIX 14 AB5 HIS A 401 ASN A 431 1 31 HELIX 15 AB6 THR B 2 HIS B 36 1 35 HELIX 16 AB7 GLN B 41 ARG B 50 1 10 HELIX 17 AB8 LEU B 52 PHE B 74 1 23 HELIX 18 AB9 PHE B 74 LEU B 85 1 12 HELIX 19 AC1 LEU B 85 TYR B 108 1 24 HELIX 20 AC2 GLY B 109 TYR B 116 1 8 HELIX 21 AC3 LEU B 117 SER B 138 1 22 HELIX 22 AC4 ASP B 153 LEU B 157 5 5 HELIX 23 AC5 LEU B 162 TYR B 185 1 24 HELIX 24 AC6 ASP B 191 GLY B 207 1 17 HELIX 25 AC7 GLY B 207 ARG B 221 1 15 HELIX 26 AC8 ASN B 224 VAL B 234 1 11 HELIX 27 AC9 VAL B 234 ARG B 254 1 21 HELIX 28 AD1 PHE B 258 TYR B 281 1 24 HELIX 29 AD2 GLU B 298 PHE B 326 1 29 HELIX 30 AD3 LEU C 767 ASP C 790 1 24 SHEET 1 AA1 2 GLU A 160 LYS A 162 0 SHEET 2 AA1 2 GLU A 165 VAL A 167 -1 O GLU A 165 N LYS A 162 SHEET 1 AA2 2 LEU A 268 LEU A 274 0 SHEET 2 AA2 2 VAL A 280 ILE A 286 -1 O LEU A 284 N LEU A 270 LINK NE2 HIS A 21 FE HEB A 502 1555 1555 2.78 LINK OE2 GLU A 101 FE HEB A 502 1555 1555 2.11 LINK NE2 HIS A 186 FE HEB A 501 1555 1555 2.30 LINK SD MET A 325 FE HEB A 501 1555 1555 2.58 LINK OE2 GLU A 378 FE HDD A 503 1555 1555 2.73 CISPEP 1 PRO A 156 GLN A 157 0 7.56 CISPEP 2 TYR B 281 PRO B 282 0 -6.00 SITE 1 AC1 17 LYS A 183 HIS A 186 THR A 190 GLY A 238 SITE 2 AC1 17 SER A 241 GLY A 242 LEU A 245 LYS A 252 SITE 3 AC1 17 MET A 325 VAL A 326 GLY A 329 ALA A 366 SITE 4 AC1 17 ALA A 369 ILE A 370 GLY A 373 TRP A 374 SITE 5 AC1 17 ALA A 377 SITE 1 AC2 17 HIS A 21 TYR A 24 ALA A 25 VAL A 65 SITE 2 AC2 17 GLY A 68 VAL A 69 GLY A 72 THR A 73 SITE 3 AC2 17 ILE A 75 GLY A 76 GLU A 101 THR A 102 SITE 4 AC2 17 PHE A 105 ILE A 146 HDD A 503 ASN B 60 SITE 5 AC2 17 VAL B 61 SITE 1 AC3 16 ARG A 11 GLU A 15 LEU A 18 THR A 19 SITE 2 AC3 16 ILE A 22 TRP A 83 ILE A 146 THR A 147 SITE 3 AC3 16 ASN A 150 MET A 153 TRP A 374 TYR A 375 SITE 4 AC3 16 GLU A 378 ARG A 381 GLN A 382 HEB A 502 CRYST1 110.060 120.860 122.720 90.00 90.00 90.00 P 21 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 0.009086 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008274 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008149 0.00000