HEADER OXIDOREDUCTASE 25-APR-22 7XMD
TITLE CRYO-EM STRUCTURE OF CYTOCHROME BO3 FROM ESCHERICHIA COLI, THE
TITLE 2 STRUCTURE COMPLEXED WITH AN ALLOSTERIC INHIBITOR N4
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CYTOCHROME BO(3) UBIQUINOL OXIDASE SUBUNIT 1;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: CYTOCHROME B562-O COMPLEX SUBUNIT I,CYTOCHROME O UBIQUINOL
COMPND 5 OXIDASE SUBUNIT 1,CYTOCHROME O SUBUNIT 1,OXIDASE BO(3) SUBUNIT 1,
COMPND 6 UBIQUINOL OXIDASE CHAIN A,UBIQUINOL OXIDASE POLYPEPTIDE I,UBIQUINOL
COMPND 7 OXIDASE SUBUNIT 1;
COMPND 8 EC: 7.1.1.3;
COMPND 9 ENGINEERED: YES;
COMPND 10 MOL_ID: 2;
COMPND 11 MOLECULE: UBIQUINOL OXIDASE SUBUNIT 2;
COMPND 12 CHAIN: B;
COMPND 13 ENGINEERED: YES;
COMPND 14 MOL_ID: 3;
COMPND 15 MOLECULE: CYTOCHROME BO(3) UBIQUINOL OXIDASE SUBUNIT 3;
COMPND 16 CHAIN: C;
COMPND 17 SYNONYM: CYTOCHROME O UBIQUINOL OXIDASE SUBUNIT 3,CYTOCHROME O
COMPND 18 SUBUNIT 3,OXIDASE BO(3) SUBUNIT 3,UBIQUINOL OXIDASE CHAIN C,UBIQUINOL
COMPND 19 OXIDASE POLYPEPTIDE III,UBIQUINOL OXIDASE SUBUNIT 3;
COMPND 20 ENGINEERED: YES;
COMPND 21 MOL_ID: 4;
COMPND 22 MOLECULE: CYTOCHROME BO(3) UBIQUINOL OXIDASE SUBUNIT 4;
COMPND 23 CHAIN: D;
COMPND 24 SYNONYM: CYTOCHROME O UBIQUINOL OXIDASE SUBUNIT 4,CYTOCHROME O
COMPND 25 SUBUNIT 4,OXIDASE BO(3) SUBUNIT 4,UBIQUINOL OXIDASE CHAIN D,UBIQUINOL
COMPND 26 OXIDASE POLYPEPTIDE IV,UBIQUINOL OXIDASE SUBUNIT 4;
COMPND 27 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_TAXID: 562;
SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 6 MOL_ID: 2;
SOURCE 7 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 8 ORGANISM_TAXID: 562;
SOURCE 9 GENE: CYOA, ACU57_11830, AM464_19145, APX88_10780, AWP93_14560,
SOURCE 10 BANRA_03634, BEA19_24285, BJI68_14080, BJJ90_20095, BK383_14750,
SOURCE 11 BMC79_002872, BO068_001687, BOB65_000403, BON66_08870, BON73_06180,
SOURCE 12 BON74_21890, BON77_14335, BON80_10695, BON86_25900, BON87_05825,
SOURCE 13 BON89_00395, BON92_15695, BON93_19065, BON98_18690, BSR05_07160,
SOURCE 14 BXT93_14110, BZL69_16590, C2121_000756, C5N07_12950, CA593_00980,
SOURCE 15 CDC27_01080, CDL36_18475, CDL37_08970, CQP61_20675, CR539_06390,
SOURCE 16 CT143_00345, CXJ73_004380, D0X26_07630, D3822_17775, D3Y67_14555,
SOURCE 17 D9E34_22950, D9J03_07430, DAH17_06675, DAH34_12595, DAH36_12985,
SOURCE 18 DD762_23785, DKP82_19825, DN627_04300, DNQ45_18500, DNX30_04955,
SOURCE 19 DTM16_23740, DTM45_11185, DU321_07410, DXT70_02705, E2119_01520,
SOURCE 20 E2122_05970, E2131_02675, E2135_01205, E4K51_12275, E5P26_04320,
SOURCE 21 E5P27_05630, E5P28_11110, E5P29_09785, E5P31_06375, E5P32_04100,
SOURCE 22 E5P34_04850, E5P35_04720, E5P36_01955, E5P40_03855, E5S36_14935,
SOURCE 23 E5S46_14035, E5S51_13330, E5S58_14090, E5S61_17450, EC3234A_4C01010,
SOURCE 24 EI021_16450, EIA08_09775, EIZ93_01035, EL79_3413, EL80_3367,
SOURCE 25 ELT17_06040, ELT20_08135, ELT41_07160, ELT49_07745, ELT51_19775,
SOURCE 26 ELU85_09175, ELV10_08020, ELV16_21785, ELX48_13290, ELX76_14920,
SOURCE 27 ELX85_08605, EVY14_00280, EXPECSC038_03272, EYV17_02895,
SOURCE 28 EYV18_09930, EYY21_23390, F2N31_13445, F3N40_15010, F9S83_01735,
SOURCE 29 F9V24_00335, FA849_16035, FA868_02450, FE587_05330, FEJ01_04230,
SOURCE 30 FEL34_02865, FGG80_03370, FGY90_08715, FHD44_10295, FJQ51_12155,
SOURCE 31 FQF29_11475, FTV93_12140, FV293_05915, FWK02_10070, G3813_001713,
SOURCE 32 G4A38_05615, G5603_08425, GIB53_01940, GKF86_04705, GKF89_04260,
SOURCE 33 GLW94_08520, GQM13_16545, GQW68_14795, GQW80_03945, GRW05_22945,
SOURCE 34 GRW57_14390, GRW81_04315, GSY44_02240, GTP88_03650, GUB08_11340,
SOURCE 35 H0O53_01600, HIN64_001359, HJQ60_002319, HJS37_002124, HJU54_001612,
SOURCE 36 HL601_03105, HLZ50_08430, HMJ82_07910, HMU48_15410, HMV41_13070,
SOURCE 37 HMV95_11775, HNC36_06575, HNC59_10400, HNC66_06810, HNC99_09295,
SOURCE 38 HND12_08495, HVW04_08795, HVX16_19275, HX136_19320, IA00_004007,
SOURCE 39 IH772_12955, IT029_003268, J0541_001708, JNP96_06590,
SOURCE 40 NCTC10082_01037, NCTC10764_05312, NCTC10974_04302, NCTC11112_03815,
SOURCE 41 NCTC12950_04133, NCTC13148_06650, NCTC8008_03342, NCTC8450_01418,
SOURCE 42 NCTC8500_04220, NCTC8621_03944, NCTC9037_03917, NCTC9044_03552,
SOURCE 43 NCTC9117_04753, PGD_02879, SAMEA3472067_03229, SAMEA3751407_02102,
SOURCE 44 WP2S18E08_34950;
SOURCE 45 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 46 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 47 MOL_ID: 3;
SOURCE 48 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 49 ORGANISM_TAXID: 562;
SOURCE 50 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 51 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 52 MOL_ID: 4;
SOURCE 53 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 54 ORGANISM_TAXID: 562;
SOURCE 55 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 56 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS RESPIRATORY ENZYME, MEMBRANE PROTEIN, HEME PROTEIN, ALLOSTERIC
KEYWDS 2 INHIBITOR, OXIDOREDUCTASE
EXPDTA ELECTRON MICROSCOPY
AUTHOR Y.NISHIDA,H.SHIGEMATSU,T.IWAMOTO,S.TAKASHIMA,Y.SHINTANI
REVDAT 2 03-JUL-24 7XMD 1 REMARK
REVDAT 1 21-DEC-22 7XMD 0
JRNL AUTH Y.NISHIDA,S.YANAGISAWA,R.MORITA,H.SHIGEMATSU,
JRNL AUTH 2 K.SHINZAWA-ITOH,H.YUKI,S.OGASAWARA,K.SHIMUTA,T.IWAMOTO,
JRNL AUTH 3 C.NAKABAYASHI,W.MATSUMURA,H.KATO,C.GOPALASINGAM,T.NAGAO,
JRNL AUTH 4 T.QAQORH,Y.TAKAHASHI,S.YAMAZAKI,K.KAMIYA,R.HARADA,N.MIZUNO,
JRNL AUTH 5 H.TAKAHASHI,Y.AKEDA,M.OHNISHI,Y.ISHII,T.KUMASAKA,T.MURATA,
JRNL AUTH 6 K.MURAMOTO,T.TOSHA,Y.SHIRO,T.HONMA,Y.SHIGETA,M.KUBO,
JRNL AUTH 7 S.TAKASHIMA,Y.SHINTANI
JRNL TITL IDENTIFYING ANTIBIOTICS BASED ON STRUCTURAL DIFFERENCES IN
JRNL TITL 2 THE CONSERVED ALLOSTERY FROM MITOCHONDRIAL HEME-COPPER
JRNL TITL 3 OXIDASES.
JRNL REF NAT COMMUN V. 13 7591 2022
JRNL REFN ESSN 2041-1723
JRNL PMID 36481732
JRNL DOI 10.1038/S41467-022-34771-Y
REMARK 2
REMARK 2 RESOLUTION. 2.99 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 SOFTWARE PACKAGES : EPU, COOT, PHENIX, PHENIX
REMARK 3 RECONSTRUCTION SCHEMA : NULL
REMARK 3
REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT
REMARK 3 PDB ENTRY : NULL
REMARK 3 REFINEMENT SPACE : NULL
REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL
REMARK 3
REMARK 3 FITTING PROCEDURE : NULL
REMARK 3
REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS
REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL
REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL
REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 2.990
REMARK 3 NUMBER OF PARTICLES : 67692
REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE
REMARK 3 CORRECTION
REMARK 3
REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL
REMARK 3
REMARK 3 OTHER DETAILS: NULL
REMARK 4
REMARK 4 7XMD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-MAY-22.
REMARK 100 THE DEPOSITION ID IS D_1300029143.
REMARK 245
REMARK 245 EXPERIMENTAL DETAILS
REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE
REMARK 245 SPECIMEN TYPE : NULL
REMARK 245
REMARK 245 ELECTRON MICROSCOPE SAMPLE
REMARK 245 SAMPLE TYPE : PARTICLE
REMARK 245 PARTICLE TYPE : POINT
REMARK 245 NAME OF SAMPLE : CYTOCHROME BO3 UBIQUINOL
REMARK 245 OXIDASE
REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 13.00
REMARK 245 SAMPLE SUPPORT DETAILS : NULL
REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL
REMARK 245 SAMPLE BUFFER : NULL
REMARK 245 PH : 7.20
REMARK 245 SAMPLE DETAILS : NULL
REMARK 245
REMARK 245 DATA ACQUISITION
REMARK 245 DATE OF EXPERIMENT : NULL
REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 7173
REMARK 245 TEMPERATURE (KELVIN) : NULL
REMARK 245 MICROSCOPE MODEL : TFS GLACIOS
REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K)
REMARK 245 MINIMUM DEFOCUS (NM) : 500.00
REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00
REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL
REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL
REMARK 245 NOMINAL CS : NULL
REMARK 245 IMAGING MODE : BRIGHT FIELD
REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00
REMARK 245 ILLUMINATION MODE : FLOOD BEAM
REMARK 245 NOMINAL MAGNIFICATION : NULL
REMARK 245 CALIBRATED MAGNIFICATION : NULL
REMARK 245 SOURCE : FIELD EMISSION GUN
REMARK 245 ACCELERATION VOLTAGE (KV) : 200
REMARK 245 IMAGING DETAILS : NULL
REMARK 247
REMARK 247 ELECTRON MICROSCOPY
REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON
REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE
REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES
REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION
REMARK 247 OF THE STRUCTURE FACTORS.
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: TETRAMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D
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 1
REMARK 465 PHE A 2
REMARK 465 GLY A 3
REMARK 465 ASN A 661
REMARK 465 GLY A 662
REMARK 465 ASN A 663
REMARK 465 MET B 1
REMARK 465 ARG B 2
REMARK 465 LEU B 3
REMARK 465 ARG B 4
REMARK 465 LYS B 5
REMARK 465 TYR B 6
REMARK 465 ASN B 7
REMARK 465 LYS B 8
REMARK 465 SER B 9
REMARK 465 LEU B 10
REMARK 465 GLY B 11
REMARK 465 TRP B 12
REMARK 465 LEU B 13
REMARK 465 SER B 14
REMARK 465 LEU B 15
REMARK 465 PHE B 16
REMARK 465 ALA B 17
REMARK 465 GLY B 18
REMARK 465 THR B 19
REMARK 465 VAL B 20
REMARK 465 LEU B 21
REMARK 465 LEU B 22
REMARK 465 HIS B 284
REMARK 465 GLY B 285
REMARK 465 LYS B 286
REMARK 465 SER B 287
REMARK 465 MET B 288
REMARK 465 ASP B 289
REMARK 465 MET B 290
REMARK 465 THR B 291
REMARK 465 GLN B 292
REMARK 465 PRO B 293
REMARK 465 GLU B 294
REMARK 465 GLY B 295
REMARK 465 GLU B 296
REMARK 465 HIS B 297
REMARK 465 SER B 298
REMARK 465 ALA B 299
REMARK 465 HIS B 300
REMARK 465 GLU B 301
REMARK 465 GLY B 302
REMARK 465 MET B 303
REMARK 465 GLU B 304
REMARK 465 GLY B 305
REMARK 465 MET B 306
REMARK 465 ASP B 307
REMARK 465 MET B 308
REMARK 465 SER B 309
REMARK 465 HIS B 310
REMARK 465 ALA B 311
REMARK 465 GLU B 312
REMARK 465 SER B 313
REMARK 465 ALA B 314
REMARK 465 HIS B 315
REMARK 465 HIS B 316
REMARK 465 HIS B 317
REMARK 465 HIS B 318
REMARK 465 HIS B 319
REMARK 465 HIS B 320
REMARK 465 HIS B 321
REMARK 465 HIS B 322
REMARK 465 HIS B 323
REMARK 465 ARG B 324
REMARK 465 MET C 1
REMARK 465 ALA C 2
REMARK 465 THR C 3
REMARK 465 ASP C 4
REMARK 465 THR C 5
REMARK 465 LEU C 6
REMARK 465 THR C 7
REMARK 465 HIS C 8
REMARK 465 ALA C 9
REMARK 465 THR C 10
REMARK 465 ALA C 11
REMARK 465 HIS C 12
REMARK 465 ALA C 13
REMARK 465 HIS C 14
REMARK 465 GLU C 15
REMARK 465 HIS C 16
REMARK 465 GLY C 17
REMARK 465 HIS C 18
REMARK 465 HIS C 19
REMARK 465 ASP C 20
REMARK 465 ALA C 21
REMARK 465 MET D 1
REMARK 465 SER D 2
REMARK 465 HIS D 3
REMARK 465 SER D 4
REMARK 465 THR D 5
REMARK 465 ASP D 6
REMARK 465 HIS D 7
REMARK 465 SER D 8
REMARK 465 GLY D 9
REMARK 465 ALA D 10
REMARK 465 SER D 11
REMARK 465 HIS D 12
REMARK 465 GLY D 13
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 NE2 HIS A 284 CE2 TYR A 288 1.42
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 6 -133.01 62.63
REMARK 500 ALA A 9 -165.62 56.41
REMARK 500 PHE A 12 -73.56 -87.89
REMARK 500 HIS A 13 26.89 -148.33
REMARK 500 LEU A 49 -5.41 70.53
REMARK 500 VAL A 114 -62.53 -121.00
REMARK 500 ALA A 172 73.62 51.35
REMARK 500 ASP A 522 36.84 -97.40
REMARK 500 ASP A 532 65.37 -159.56
REMARK 500 ASN A 551 -7.13 69.10
REMARK 500 GLU A 572 52.62 -92.87
REMARK 500 ALA A 657 -166.97 -117.04
REMARK 500 ASP B 31 63.86 -158.41
REMARK 500 ARG B 70 -139.81 40.76
REMARK 500 ALA B 71 -27.93 -152.32
REMARK 500 ASN B 81 17.00 49.86
REMARK 500 SER B 83 -62.52 -95.09
REMARK 500 LEU B 120 -11.07 72.66
REMARK 500 MET B 134 -160.75 -123.11
REMARK 500 ILE B 183 130.15 15.01
REMARK 500 GLN B 240 49.49 -81.67
REMARK 500 TYR B 260 75.58 -102.01
REMARK 500 MET C 128 53.87 -91.43
REMARK 500 ALA C 203 34.39 -99.81
REMARK 500 PRO D 43 43.14 -76.61
REMARK 500 ALA D 44 -38.09 -132.13
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 702 FE
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 106 NE2
REMARK 620 2 HEM A 702 NA 97.1
REMARK 620 3 HEM A 702 NB 79.2 87.7
REMARK 620 4 HEM A 702 NC 82.1 174.1 86.4
REMARK 620 5 HEM A 702 ND 102.0 94.1 177.7 91.8
REMARK 620 6 HIS A 421 NE2 167.6 91.7 92.5 88.2 86.0
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CU A 703 CU
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 284 ND1
REMARK 620 2 HIS A 333 NE2 104.4
REMARK 620 3 HIS A 334 NE2 107.7 75.4
REMARK 620 N 1 2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 HEO A 701 FE
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 419 NE2
REMARK 620 2 HEO A 701 NA 84.7
REMARK 620 3 HEO A 701 NB 93.5 87.5
REMARK 620 4 HEO A 701 NC 100.9 171.7 86.0
REMARK 620 5 HEO A 701 ND 94.5 94.6 171.9 91.2
REMARK 620 N 1 2 3 4
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: EMD-33294 RELATED DB: EMDB
REMARK 900 CRYO-EM STRUCTURE OF CYTOCHROME BO3 FROM ESCHERICHIA COLI, THE
REMARK 900 STRUCTURE COMPLEXED WITH AN ALLOSTERIC INHIBITOR N4
DBREF 7XMD A 1 663 UNP P0ABI8 CYOB_ECOLI 1 663
DBREF1 7XMD B 1 315 UNP A0A024L5V9_ECOLX
DBREF2 7XMD B A0A024L5V9 1 315
DBREF 7XMD C 1 204 UNP P0ABJ3 CYOC_ECOLI 1 204
DBREF 7XMD D 1 109 UNP P0ABJ6 CYOD_ECOLI 1 109
SEQADV 7XMD HIS B 316 UNP A0A024L5V EXPRESSION TAG
SEQADV 7XMD HIS B 317 UNP A0A024L5V EXPRESSION TAG
SEQADV 7XMD HIS B 318 UNP A0A024L5V EXPRESSION TAG
SEQADV 7XMD HIS B 319 UNP A0A024L5V EXPRESSION TAG
SEQADV 7XMD HIS B 320 UNP A0A024L5V EXPRESSION TAG
SEQADV 7XMD HIS B 321 UNP A0A024L5V EXPRESSION TAG
SEQADV 7XMD HIS B 322 UNP A0A024L5V EXPRESSION TAG
SEQADV 7XMD HIS B 323 UNP A0A024L5V EXPRESSION TAG
SEQADV 7XMD ARG B 324 UNP A0A024L5V EXPRESSION TAG
SEQRES 1 A 663 MET PHE GLY LYS LEU SER LEU ASP ALA VAL PRO PHE HIS
SEQRES 2 A 663 GLU PRO ILE VAL MET VAL THR ILE ALA GLY ILE ILE LEU
SEQRES 3 A 663 GLY GLY LEU ALA LEU VAL GLY LEU ILE THR TYR PHE GLY
SEQRES 4 A 663 LYS TRP THR TYR LEU TRP LYS GLU TRP LEU THR SER VAL
SEQRES 5 A 663 ASP HIS LYS ARG LEU GLY ILE MET TYR ILE ILE VAL ALA
SEQRES 6 A 663 ILE VAL MET LEU LEU ARG GLY PHE ALA ASP ALA ILE MET
SEQRES 7 A 663 MET ARG SER GLN GLN ALA LEU ALA SER ALA GLY GLU ALA
SEQRES 8 A 663 GLY PHE LEU PRO PRO HIS HIS TYR ASP GLN ILE PHE THR
SEQRES 9 A 663 ALA HIS GLY VAL ILE MET ILE PHE PHE VAL ALA MET PRO
SEQRES 10 A 663 PHE VAL ILE GLY LEU MET ASN LEU VAL VAL PRO LEU GLN
SEQRES 11 A 663 ILE GLY ALA ARG ASP VAL ALA PHE PRO PHE LEU ASN ASN
SEQRES 12 A 663 LEU SER PHE TRP PHE THR VAL VAL GLY VAL ILE LEU VAL
SEQRES 13 A 663 ASN VAL SER LEU GLY VAL GLY GLU PHE ALA GLN THR GLY
SEQRES 14 A 663 TRP LEU ALA TYR PRO PRO LEU SER GLY ILE GLU TYR SER
SEQRES 15 A 663 PRO GLY VAL GLY VAL ASP TYR TRP ILE TRP SER LEU GLN
SEQRES 16 A 663 LEU SER GLY ILE GLY THR THR LEU THR GLY ILE ASN PHE
SEQRES 17 A 663 PHE VAL THR ILE LEU LYS MET ARG ALA PRO GLY MET THR
SEQRES 18 A 663 MET PHE LYS MET PRO VAL PHE THR TRP ALA SER LEU CYS
SEQRES 19 A 663 ALA ASN VAL LEU ILE ILE ALA SER PHE PRO ILE LEU THR
SEQRES 20 A 663 VAL THR VAL ALA LEU LEU THR LEU ASP ARG TYR LEU GLY
SEQRES 21 A 663 THR HIS PHE PHE THR ASN ASP MET GLY GLY ASN MET MET
SEQRES 22 A 663 MET TYR ILE ASN LEU ILE TRP ALA TRP GLY HIS PRO GLU
SEQRES 23 A 663 VAL TYR ILE LEU ILE LEU PRO VAL PHE GLY VAL PHE SER
SEQRES 24 A 663 GLU ILE ALA ALA THR PHE SER ARG LYS ARG LEU PHE GLY
SEQRES 25 A 663 TYR THR SER LEU VAL TRP ALA THR VAL CYS ILE THR VAL
SEQRES 26 A 663 LEU SER PHE ILE VAL TRP LEU HIS HIS PHE PHE THR MET
SEQRES 27 A 663 GLY ALA GLY ALA ASN VAL ASN ALA PHE PHE GLY ILE THR
SEQRES 28 A 663 THR MET ILE ILE ALA ILE PRO THR GLY VAL LYS ILE PHE
SEQRES 29 A 663 ASN TRP LEU PHE THR MET TYR GLN GLY ARG ILE VAL PHE
SEQRES 30 A 663 HIS SER ALA MET LEU TRP THR ILE GLY PHE ILE VAL THR
SEQRES 31 A 663 PHE SER VAL GLY GLY MET THR GLY VAL LEU LEU ALA VAL
SEQRES 32 A 663 PRO GLY ALA ASP PHE VAL LEU HIS ASN SER LEU PHE LEU
SEQRES 33 A 663 ILE ALA HIS PHE HIS ASN VAL ILE ILE GLY GLY VAL VAL
SEQRES 34 A 663 PHE GLY CYS PHE ALA GLY MET THR TYR TRP TRP PRO LYS
SEQRES 35 A 663 ALA PHE GLY PHE LYS LEU ASN GLU THR TRP GLY LYS ARG
SEQRES 36 A 663 ALA PHE TRP PHE TRP ILE ILE GLY PHE PHE VAL ALA PHE
SEQRES 37 A 663 MET PRO LEU TYR ALA LEU GLY PHE MET GLY MET THR ARG
SEQRES 38 A 663 ARG LEU SER GLN GLN ILE ASP PRO GLN PHE HIS THR MET
SEQRES 39 A 663 LEU MET ILE ALA ALA SER GLY ALA VAL LEU ILE ALA LEU
SEQRES 40 A 663 GLY ILE LEU CYS LEU VAL ILE GLN MET TYR VAL SER ILE
SEQRES 41 A 663 ARG ASP ARG ASP GLN ASN ARG ASP LEU THR GLY ASP PRO
SEQRES 42 A 663 TRP GLY GLY ARG THR LEU GLU TRP ALA THR SER SER PRO
SEQRES 43 A 663 PRO PRO PHE TYR ASN PHE ALA VAL VAL PRO HIS VAL HIS
SEQRES 44 A 663 GLU ARG ASP ALA PHE TRP GLU MET LYS GLU LYS GLY GLU
SEQRES 45 A 663 ALA TYR LYS LYS PRO ASP HIS TYR GLU GLU ILE HIS MET
SEQRES 46 A 663 PRO LYS ASN SER GLY ALA GLY ILE VAL ILE ALA ALA PHE
SEQRES 47 A 663 SER THR ILE PHE GLY PHE ALA MET ILE TRP HIS ILE TRP
SEQRES 48 A 663 TRP LEU ALA ILE VAL GLY PHE ALA GLY MET ILE ILE THR
SEQRES 49 A 663 TRP ILE VAL LYS SER PHE ASP GLU ASP VAL ASP TYR TYR
SEQRES 50 A 663 VAL PRO VAL ALA GLU ILE GLU LYS LEU GLU ASN GLN HIS
SEQRES 51 A 663 PHE ASP GLU ILE THR LYS ALA GLY LEU LYS ASN GLY ASN
SEQRES 1 B 324 MET ARG LEU ARG LYS TYR ASN LYS SER LEU GLY TRP LEU
SEQRES 2 B 324 SER LEU PHE ALA GLY THR VAL LEU LEU SER GLY CYS ASN
SEQRES 3 B 324 SER ALA LEU LEU ASP PRO LYS GLY GLN ILE GLY LEU GLU
SEQRES 4 B 324 GLN ARG SER LEU ILE LEU THR ALA PHE GLY LEU MET LEU
SEQRES 5 B 324 ILE VAL VAL ILE PRO ALA ILE LEU MET ALA VAL GLY PHE
SEQRES 6 B 324 ALA TRP LYS TYR ARG ALA SER ASN LYS ASP ALA LYS TYR
SEQRES 7 B 324 SER PRO ASN TRP SER HIS SER ASN LYS VAL GLU ALA VAL
SEQRES 8 B 324 VAL TRP THR VAL PRO ILE LEU ILE ILE ILE PHE LEU ALA
SEQRES 9 B 324 VAL LEU THR TRP LYS THR THR HIS ALA LEU GLU PRO SER
SEQRES 10 B 324 LYS PRO LEU ALA HIS ASP GLU LYS PRO ILE THR ILE GLU
SEQRES 11 B 324 VAL VAL SER MET ASP TRP LYS TRP PHE PHE ILE TYR PRO
SEQRES 12 B 324 GLU GLN GLY ILE ALA THR VAL ASN GLU ILE ALA PHE PRO
SEQRES 13 B 324 ALA ASN THR PRO VAL TYR PHE LYS VAL THR SER ASN SER
SEQRES 14 B 324 VAL MET ASN SER PHE PHE ILE PRO ARG LEU GLY SER GLN
SEQRES 15 B 324 ILE TYR ALA MET ALA GLY MET GLN THR ARG LEU HIS LEU
SEQRES 16 B 324 ILE ALA ASN GLU PRO GLY THR TYR ASP GLY ILE SER ALA
SEQRES 17 B 324 SER TYR SER GLY PRO GLY PHE SER GLY MET LYS PHE LYS
SEQRES 18 B 324 ALA ILE ALA THR PRO ASP ARG ALA ALA PHE ASP GLN TRP
SEQRES 19 B 324 VAL ALA LYS ALA LYS GLN SER PRO ASN THR MET SER ASP
SEQRES 20 B 324 MET ALA ALA PHE GLU LYS LEU ALA ALA PRO SER GLU TYR
SEQRES 21 B 324 ASN GLN VAL GLU TYR PHE SER ASN VAL LYS PRO ASP LEU
SEQRES 22 B 324 PHE ALA ASP VAL ILE ASN LYS PHE MET ALA HIS GLY LYS
SEQRES 23 B 324 SER MET ASP MET THR GLN PRO GLU GLY GLU HIS SER ALA
SEQRES 24 B 324 HIS GLU GLY MET GLU GLY MET ASP MET SER HIS ALA GLU
SEQRES 25 B 324 SER ALA HIS HIS HIS HIS HIS HIS HIS HIS HIS ARG
SEQRES 1 C 204 MET ALA THR ASP THR LEU THR HIS ALA THR ALA HIS ALA
SEQRES 2 C 204 HIS GLU HIS GLY HIS HIS ASP ALA GLY GLY THR LYS ILE
SEQRES 3 C 204 PHE GLY PHE TRP ILE TYR LEU MET SER ASP CYS ILE LEU
SEQRES 4 C 204 PHE SER ILE LEU PHE ALA THR TYR ALA VAL LEU VAL ASN
SEQRES 5 C 204 GLY THR ALA GLY GLY PRO THR GLY LYS ASP ILE PHE GLU
SEQRES 6 C 204 LEU PRO PHE VAL LEU VAL GLU THR PHE LEU LEU LEU PHE
SEQRES 7 C 204 SER SER ILE THR TYR GLY MET ALA ALA ILE ALA MET TYR
SEQRES 8 C 204 LYS ASN ASN LYS SER GLN VAL ILE SER TRP LEU ALA LEU
SEQRES 9 C 204 THR TRP LEU PHE GLY ALA GLY PHE ILE GLY MET GLU ILE
SEQRES 10 C 204 TYR GLU PHE HIS HIS LEU ILE VAL ASN GLY MET GLY PRO
SEQRES 11 C 204 ASP ARG SER GLY PHE LEU SER ALA PHE PHE ALA LEU VAL
SEQRES 12 C 204 GLY THR HIS GLY LEU HIS VAL THR SER GLY LEU ILE TRP
SEQRES 13 C 204 MET ALA VAL LEU MET VAL GLN ILE ALA ARG ARG GLY LEU
SEQRES 14 C 204 THR SER THR ASN ARG THR ARG ILE MET CYS LEU SER LEU
SEQRES 15 C 204 PHE TRP HIS PHE LEU ASP VAL VAL TRP ILE CYS VAL PHE
SEQRES 16 C 204 THR VAL VAL TYR LEU MET GLY ALA MET
SEQRES 1 D 109 MET SER HIS SER THR ASP HIS SER GLY ALA SER HIS GLY
SEQRES 2 D 109 SER VAL LYS THR TYR MET THR GLY PHE ILE LEU SER ILE
SEQRES 3 D 109 ILE LEU THR VAL ILE PRO PHE TRP MET VAL MET THR GLY
SEQRES 4 D 109 ALA ALA SER PRO ALA VAL ILE LEU GLY THR ILE LEU ALA
SEQRES 5 D 109 MET ALA VAL VAL GLN VAL LEU VAL HIS LEU VAL CYS PHE
SEQRES 6 D 109 LEU HIS MET ASN THR LYS SER ASP GLU GLY TRP ASN MET
SEQRES 7 D 109 THR ALA PHE VAL PHE THR VAL LEU ILE ILE ALA ILE LEU
SEQRES 8 D 109 VAL VAL GLY SER ILE TRP ILE MET TRP ASN LEU ASN TYR
SEQRES 9 D 109 ASN MET MET MET HIS
HET HEO A 701 59
HET HEM A 702 43
HET CU A 703 1
HET PEE A 704 51
HET JYR A 705 17
HET UNX B 401 1
HET PEE C 301 51
HETNAM HEO HEME O
HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE
HETNAM CU COPPER (II) ION
HETNAM PEE 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
HETNAM JYR METHYL 3-OXIDANYL-5-[OXIDANYL(OXIDANYLIDENE)-$L^{4}-
HETNAM 2 JYR AZANYL]-1-BENZOTHIOPHENE-2-CARBOXYLATE
HETNAM UNX UNKNOWN ATOM OR ION
HETSYN HEM HEME
HETSYN PEE DOPE
FORMUL 5 HEO C49 H58 FE N4 O5 2+
FORMUL 6 HEM C34 H32 FE N4 O4
FORMUL 7 CU CU 2+
FORMUL 8 PEE 2(C41 H78 N O8 P)
FORMUL 9 JYR C10 H7 N O5 S
FORMUL 10 UNX X
HELIX 1 AA1 MET A 18 PHE A 38 1 21
HELIX 2 AA2 TRP A 41 GLU A 47 1 7
HELIX 3 AA3 ASP A 53 SER A 87 1 35
HELIX 4 AA4 PRO A 95 VAL A 114 1 20
HELIX 5 AA5 VAL A 114 ILE A 131 1 18
HELIX 6 AA6 PHE A 138 LEU A 160 1 23
HELIX 7 AA7 TYR A 173 GLY A 178 1 6
HELIX 8 AA8 VAL A 185 MET A 215 1 31
HELIX 9 AA9 PRO A 226 LEU A 259 1 34
HELIX 10 AB1 MET A 272 HIS A 284 1 13
HELIX 11 AB2 HIS A 284 SER A 306 1 23
HELIX 12 AB3 GLY A 312 SER A 327 1 16
HELIX 13 AB4 PHE A 328 ILE A 329 5 2
HELIX 14 AB5 VAL A 330 GLY A 339 5 10
HELIX 15 AB6 GLY A 341 ILE A 355 1 15
HELIX 16 AB7 ILE A 355 MET A 370 1 16
HELIX 17 AB8 HIS A 378 VAL A 403 1 26
HELIX 18 AB9 VAL A 403 HIS A 411 1 9
HELIX 19 AC1 SER A 413 GLY A 426 1 14
HELIX 20 AC2 GLY A 427 TRP A 440 1 14
HELIX 21 AC3 TRP A 440 GLY A 445 1 6
HELIX 22 AC4 ASN A 449 GLY A 478 1 30
HELIX 23 AC5 ASP A 488 GLN A 490 5 3
HELIX 24 AC6 PHE A 491 ASP A 522 1 32
HELIX 25 AC7 THR A 538 THR A 543 5 6
HELIX 26 AC8 ASP A 562 GLY A 571 1 10
HELIX 27 AC9 GLY A 590 TRP A 608 1 19
HELIX 28 AD1 ILE A 610 ASP A 631 1 22
HELIX 29 AD2 PRO A 639 LYS A 656 1 18
HELIX 30 AD3 GLY B 34 ARG B 70 1 37
HELIX 31 AD4 SER B 85 LEU B 114 1 30
HELIX 32 AD5 GLY B 212 MET B 218 5 7
HELIX 33 AD6 ASP B 227 GLN B 240 1 14
HELIX 34 AD7 ASP B 247 ALA B 255 1 9
HELIX 35 AD8 ASP B 272 ALA B 283 1 12
HELIX 36 AD9 GLY C 23 VAL C 51 1 29
HELIX 37 AE1 GLU C 65 LYS C 92 1 28
HELIX 38 AE2 ASN C 94 ASN C 126 1 33
HELIX 39 AE3 SER C 133 GLY C 168 1 36
HELIX 40 AE4 THR C 170 VAL C 198 1 29
HELIX 41 AE5 LEU C 200 MET C 204 5 5
HELIX 42 AE6 VAL D 15 GLY D 39 1 25
HELIX 43 AE7 ALA D 44 CYS D 64 1 21
HELIX 44 AE8 LYS D 71 GLY D 75 5 5
HELIX 45 AE9 ASN D 77 MET D 106 1 30
SHEET 1 AA1 2 ILE A 583 PRO A 586 0
SHEET 2 AA1 2 ASP A 635 VAL A 638 -1 O TYR A 636 N MET A 585
SHEET 1 AA2 6 THR B 191 ILE B 196 0
SHEET 2 AA2 6 PRO B 160 SER B 167 -1 N PHE B 163 O LEU B 193
SHEET 3 AA2 6 ILE B 127 SER B 133 1 N ILE B 127 O PRO B 160
SHEET 4 AA2 6 TRP B 138 ILE B 141 -1 O ILE B 141 N GLU B 130
SHEET 5 AA2 6 ALA B 148 VAL B 150 -1 O THR B 149 N PHE B 140
SHEET 6 AA2 6 GLU B 264 PHE B 266 -1 O PHE B 266 N ALA B 148
SHEET 1 AA3 5 GLU B 152 PRO B 156 0
SHEET 2 AA3 5 PHE B 220 THR B 225 1 O ILE B 223 N ILE B 153
SHEET 3 AA3 5 GLY B 201 SER B 207 -1 N GLY B 201 O ALA B 224
SHEET 4 AA3 5 ASN B 172 PHE B 175 -1 N PHE B 175 O ILE B 206
SHEET 5 AA3 5 TYR B 184 ALA B 185 -1 O ALA B 185 N ASN B 172
LINK NE2 HIS A 106 FE HEM A 702 1555 1555 1.99
LINK ND1 HIS A 284 CU CU A 703 1555 1555 2.00
LINK NE2 HIS A 333 CU CU A 703 1555 1555 2.00
LINK NE2 HIS A 334 CU CU A 703 1555 1555 2.00
LINK NE2 HIS A 419 FE HEO A 701 1555 1555 2.05
LINK NE2 HIS A 421 FE HEM A 702 1555 1555 1.97
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1
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 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000