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- PDB-7coh: Dimeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Ox... -

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Basic information

Entry
Database: PDB / ID: 7coh
TitleDimeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Oxidized State
Components(Cytochrome c oxidase subunit ...) x 13
KeywordsOXIDOREDUCTASE / Dimer / Fully Oxidized
Function / homology
Function and homology information


TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / respiratory chain complex IV / Respiratory electron transport / regulation of oxidative phosphorylation / mitochondrial respiratory chain complex IV / mitochondrial respirasome / cytochrome-c oxidase ...TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / respiratory chain complex IV / Respiratory electron transport / regulation of oxidative phosphorylation / mitochondrial respiratory chain complex IV / mitochondrial respirasome / cytochrome-c oxidase / oxidative phosphorylation / mitochondrial electron transport, cytochrome c to oxygen / electron transport coupled proton transport / cytochrome-c oxidase activity / ATP synthesis coupled electron transport / enzyme regulator activity / central nervous system development / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit 8 superfamily / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit VIIa superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily ...Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit 8 superfamily / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit VIIa superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / Cytochrome c oxidase subunit VIc / Cytochrome C oxidase chain VIIB / : / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase subunit Va / Cytochrome c oxidase, subunit VIb / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase subunit I domain / Cytochrome c oxidase, subunit II / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Cupredoxin
Similarity search - Domain/homology
CARDIOLIPIN / CHOLIC ACID / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / EICOSANE / Chem-PEK / PEROXIDE ION / Chem-PGV / Cytochrome c oxidase subunit 1 ...CARDIOLIPIN / CHOLIC ACID / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / EICOSANE / Chem-PEK / PEROXIDE ION / Chem-PGV / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase subunit 6C / Cytochrome c oxidase subunit 7A1, mitochondrial / Cytochrome c oxidase subunit 6A2, mitochondrial / Cytochrome c oxidase subunit 8B, mitochondrial / Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsShinzawa-Itoh, K. / Muramoto, K.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP17H03646 Japan
Japan Society for the Promotion of Science (JSPS)JP22370060 Japan
Japan Society for the Promotion of Science (JSPS)JP18K06162 Japan
CitationJournal: Biochim.Biophys.Acta / Year: 2021
Title: The 1.3-A Resolution structure of bovine cytochrome c oxidase suggests a dimerization mechanism
Authors: Shinzawa-Itoh, K. / Hatanaka, M. / Fujita, K. / Yano, N. / Ogasawara, Y. / Iwata, J. / Yamashita, E. / Tsukihara, T. / Yoshikawa, S. / Muramoto, K.
History
DepositionAug 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_validate_chiral
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c oxidase subunit 1
B: Cytochrome c oxidase subunit 2
C: Cytochrome c oxidase subunit 3
D: Cytochrome c oxidase subunit 4 isoform 1
E: Cytochrome c oxidase subunit 5A
F: Cytochrome c oxidase subunit 5B
G: Cytochrome c oxidase subunit 6A2, mitochondrial
H: Cytochrome c oxidase subunit 6B1
I: Cytochrome c oxidase subunit 6C
J: Cytochrome c oxidase subunit 7A1
K: Cytochrome c oxidase subunit 7B
L: Cytochrome c oxidase subunit 7C, mitochondrial
M: Cytochrome c oxidase subunit 8B
N: Cytochrome c oxidase subunit 1
O: Cytochrome c oxidase subunit 2
P: Cytochrome c oxidase subunit 3
Q: Cytochrome c oxidase subunit 4 isoform 1
R: Cytochrome c oxidase subunit 5A
S: Cytochrome c oxidase subunit 5B
T: Cytochrome c oxidase subunit 6A2, mitochondrial
U: Cytochrome c oxidase subunit 6B1
V: Cytochrome c oxidase subunit 6C
W: Cytochrome c oxidase subunit 7A1
X: Cytochrome c oxidase subunit 7B
Y: Cytochrome c oxidase subunit 7C, mitochondrial
Z: Cytochrome c oxidase subunit 8B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)460,733159
Polymers409,97226
Non-polymers50,762133
Water36,1562007
1
A: Cytochrome c oxidase subunit 1
B: Cytochrome c oxidase subunit 2
C: Cytochrome c oxidase subunit 3
D: Cytochrome c oxidase subunit 4 isoform 1
E: Cytochrome c oxidase subunit 5A
F: Cytochrome c oxidase subunit 5B
G: Cytochrome c oxidase subunit 6A2, mitochondrial
H: Cytochrome c oxidase subunit 6B1
I: Cytochrome c oxidase subunit 6C
J: Cytochrome c oxidase subunit 7A1
K: Cytochrome c oxidase subunit 7B
L: Cytochrome c oxidase subunit 7C, mitochondrial
M: Cytochrome c oxidase subunit 8B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,33679
Polymers204,98613
Non-polymers25,35066
Water16,232901
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
N: Cytochrome c oxidase subunit 1
O: Cytochrome c oxidase subunit 2
P: Cytochrome c oxidase subunit 3
Q: Cytochrome c oxidase subunit 4 isoform 1
R: Cytochrome c oxidase subunit 5A
S: Cytochrome c oxidase subunit 5B
T: Cytochrome c oxidase subunit 6A2, mitochondrial
U: Cytochrome c oxidase subunit 6B1
V: Cytochrome c oxidase subunit 6C
W: Cytochrome c oxidase subunit 7A1
X: Cytochrome c oxidase subunit 7B
Y: Cytochrome c oxidase subunit 7C, mitochondrial
Z: Cytochrome c oxidase subunit 8B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,39880
Polymers204,98613
Non-polymers25,41267
Water13,241735
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)181.998, 204.193, 177.759
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21N
12B
22O
13C
23P
14D
24Q
15E
25R
16F
26S
17G
27T
18H
28U
19I
29V
110J
210W
111K
211X
112L
212Y
113M
213Z

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 526
2116N1 - 526
1126B1 - 227
2126O1 - 227
1136C4 - 272
2136P4 - 272
1146D4 - 146
2146Q4 - 146
1156E7 - 108
2156R7 - 108
1166F3 - 99
2166S3 - 99
1176G12 - 83
2176T12 - 83
1186H11 - 85
2186U11 - 85
1196I3 - 72
2196V3 - 72
11106J1 - 56
21106W1 - 56
11116K6 - 54
21116X6 - 54
11126L3 - 46
21126Y3 - 46
11136M1 - 40
21136Z1 - 40

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.992874, -0.004209, 0.119096), (-0.000825, -0.999109, -0.042192), (0.119167, -0.041989, 0.991986)164.909286, 626.181702, 3.40094
3given(1), (1), (1)
4given(-0.993064, 0.000737, 0.117572), (-0.006167, -0.99893, -0.045827), (0.117413, -0.046234, 0.992006)163.56012, 627.472656, 5.05428
5given(1), (1), (1)
6given(-0.992644, -0.000555, 0.121069), (-0.004651, -0.999077, -0.042712), (0.120981, -0.042961, 0.991725)163.385391, 626.700867, 3.53765
7given(1), (1), (1)
8given(-0.993121, -0.009236, 0.116729), (0.005687, -0.999512, -0.030699), (0.116956, -0.029823, 0.992689)167.011475, 623.344543, -0.12926
9given(1), (1), (1)
10given(-0.989065, -0.048193, 0.139382), (0.041678, -0.997914, -0.049291), (0.141467, -0.042943, 0.989011)174.097092, 621.956238, 1.58451
11given(1), (1), (1)
12given(-0.992978, -0.007816, 0.11804), (0.00355, -0.999334, -0.036306), (0.118245, -0.035632, 0.992345)166.351074, 624.475769, 1.46164
13given(1), (1), (1)
14given(-0.992674, -0.003588, 0.120769), (-0.001624, -0.999073, -0.043026), (0.120812, -0.042906, 0.991748)164.317001, 626.455872, 3.54662
15given(1), (1), (1)
16given(-0.992199, -0.000173, 0.124663), (-0.00553, -0.998954, -0.045397), (0.12454, -0.045732, 0.99116)162.653839, 627.273132, 4.10646
17given(1), (1), (1)
18given(-0.994219, -0.016933, 0.106026), (0.013143, -0.999253, -0.036346), (0.106562, -0.034742, 0.993699)171.533722, 623.327332, 2.43378
19given(1), (1), (1)
20given(-0.992775, 0.004855, 0.119889), (-0.010977, -0.998666, -0.050455), (0.119484, -0.051406, 0.991504)162.190308, 628.970703, 6.23286
21given(1), (1), (1)
22given(-0.993621, 0.004438, 0.112682), (-0.007432, -0.99963, -0.026169), (0.112524, -0.026839, 0.993286)163.377777, 624.583435, -0.59852
23given(1), (1), (1)
24given(-0.992657, -0.009419, 0.120592), (0.004188, -0.999042, -0.043556), (0.120887, -0.042731, 0.991746)166.12204, 625.789307, 3.38452
25given(1), (1), (1)
26given(-0.992883, -0.017581, 0.117792), (0.012109, -0.998821, -0.047014), (0.118479, -0.045253, 0.991925)169.179886, 625.112427, 4.35528

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Components

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Cytochrome c oxidase subunit ... , 13 types, 26 molecules ANBOCPDQERFSGTHUIVJWKXLYMZ

#1: Protein Cytochrome c oxidase subunit 1 / / Cytochrome c oxidase polypeptide I


Mass: 57093.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: MT-CO1, COI, COXI, MTCO1 / Production host: Bos taurus (cattle) / References: UniProt: P00396, cytochrome-c oxidase
#2: Protein Cytochrome c oxidase subunit 2 / / Cytochrome c oxidase polypeptide II


Mass: 26068.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Bos taurus (cattle) / References: UniProt: P68530, cytochrome-c oxidase
#3: Protein Cytochrome c oxidase subunit 3 / / Cytochrome c oxidase polypeptide III


Mass: 29957.627 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: MT-CO3, COIII, COXIII, MTCO3 / Production host: Bos taurus (cattle) / References: UniProt: P00415, cytochrome-c oxidase
#4: Protein Cytochrome c oxidase subunit 4 isoform 1 / / Cytochrome c oxidase polypeptide IV


Mass: 17179.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: COX4I1, COX4 / Production host: Bos taurus (cattle) / References: UniProt: P00423
#5: Protein Cytochrome c oxidase subunit 5A / / Cytochrome c oxidase polypeptide Va


Mass: 12453.081 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: COX5A / Production host: Bos taurus (cattle) / References: UniProt: P00426
#6: Protein Cytochrome c oxidase subunit 5B / / Cytochrome c oxidase polypeptide VIa


Mass: 10684.038 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Bos taurus (cattle) / References: UniProt: P00428
#7: Protein Cytochrome c oxidase subunit 6A2, mitochondrial / / Cytochrome c oxidase polypeptide VIa-heart / COXVIAH / Cytochrome c oxidase polypeptide VIb


Mass: 9549.802 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: COX6A2, COX6A / Production host: Bos taurus (cattle) / References: UniProt: P07471
#8: Protein Cytochrome c oxidase subunit 6B1 / / Cytochrome c oxidase polypeptide VII


Mass: 10039.244 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: COX6B1, COX6B / Production host: Bos taurus (cattle) / References: UniProt: P00429
#9: Protein Cytochrome c oxidase subunit 6C / / Cytochrome c oxidase polypeptide VIc / Cytochrome c oxidase subunit STA


Mass: 8494.982 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: COX6C / Production host: Bos taurus (cattle) / References: UniProt: P04038
#10: Protein Cytochrome c oxidase subunit 7A1 / / Cytochrome c oxidase subunit VIIIc / VIIIC


Mass: 6682.726 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: COX7A1, COX7A, COX7AH / Production host: Bos taurus (cattle) / References: UniProt: P07470
#11: Protein Cytochrome c oxidase subunit 7B / / Cytochrome c oxidase polypeptide VIIb


Mass: 6365.217 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: COX7B / Production host: Bos taurus (cattle) / References: UniProt: P13183
#12: Protein/peptide Cytochrome c oxidase subunit 7C, mitochondrial / / Cytochrome c oxidase polypeptide VIIIA


Mass: 5449.396 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: COX7C, COX7CP1 / Production host: Bos taurus (cattle) / References: UniProt: P00430
#13: Protein/peptide Cytochrome c oxidase subunit 8B / / Cytochrome c oxidase polypeptide VIII-heart


Mass: 4967.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: COX8B, COX8H / Production host: Bos taurus (cattle) / References: UniProt: P10175

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Sugars , 1 types, 42 molecules

#20: Sugar...
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: C22H42O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM

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Non-polymers , 15 types, 2098 molecules

#14: Chemical
ChemComp-HEA / HEME-A / Heme A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#15: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#16: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#17: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#18: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#19: Chemical
ChemComp-CHD / CHOLIC ACID / Cholic acid


Mass: 408.571 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H40O5 / Feature type: SUBJECT OF INVESTIGATION
#21: Chemical ChemComp-PER / PEROXIDE ION / Peroxide


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#22: Chemical...
ChemComp-LFA / EICOSANE / LIPID FRAGMENT / Icosane


Mass: 282.547 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: C20H42 / Feature type: SUBJECT OF INVESTIGATION
#23: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C2H6O2
#24: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2
#25: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 749.007 Da / Num. of mol.: 2 / Source method: obtained synthetically
#26: Chemical ChemComp-PEK / (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE / PHOSPHATIDYLETHANOLAMINE / 2-ARACHIDONOYL-1-STEAROYL-SN-GLYCEROL-3-PHOSPHOETHANOLAMINE / Phosphatidylethanolamine


Mass: 768.055 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C43H78NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#27: Chemical
ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL / Phosphatidylglycerol


Mass: 749.007 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H77O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#28: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#29: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2007 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 277 K / Method: batch mode / pH: 6.8
Details: 40 mM sodium phosphate pH 6.8, 0.2% decylmaltoside, 1% polyethylene glycol 4000, 2% ethylene glycol

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Data collection

DiffractionMean temperature: 60 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.3→200 Å / Num. obs: 1596005 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.55 / Rpim(I) all: 0.03 / Net I/σ(I): 39.7
Reflection shellResolution: 1.3→1.31 Å / Num. unique obs: 39643 / Rpim(I) all: 0.94

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B1A

5b1a


Resolution: 1.3→40 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.771 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1704 79183 5 %RANDOM
Rwork0.1485 ---
obs0.1496 1510822 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 158.86 Å2 / Biso mean: 30.499 Å2 / Biso min: 13.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å2-0 Å20 Å2
2---1.58 Å20 Å2
3---1.12 Å2
Refinement stepCycle: final / Resolution: 1.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27834 0 2608 2080 32522
Biso mean--50.74 40.92 -
Num. residues----3474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.01531953
X-RAY DIFFRACTIONr_bond_other_d0.0030.01730504
X-RAY DIFFRACTIONr_angle_refined_deg2.271.66843078
X-RAY DIFFRACTIONr_angle_other_deg1.5261.58470978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17253573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.91121.71359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.983154675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.27115124
X-RAY DIFFRACTIONr_chiral_restr0.4660.24065
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0233225
X-RAY DIFFRACTIONr_gen_planes_other0.0060.026798
X-RAY DIFFRACTIONr_rigid_bond_restr5.786362383
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A8860LOOSE POSITIONAL0.195
1A8860LOOSE THERMAL5.2110
2B3671LOOSE POSITIONAL0.375
2B3671LOOSE THERMAL9.1310
3C4854LOOSE POSITIONAL0.235
3C4854LOOSE THERMAL5.610
4D2242LOOSE POSITIONAL0.395
4D2242LOOSE THERMAL12.5210
5E1628LOOSE POSITIONAL0.445
5E1628LOOSE THERMAL8.9210
6F1380LOOSE POSITIONAL0.315
6F1380LOOSE THERMAL5.5310
7G1160LOOSE POSITIONAL0.425
7G1160LOOSE THERMAL7.8810
8H1180LOOSE POSITIONAL0.245
8H1180LOOSE THERMAL8.910
9I1147LOOSE POSITIONAL0.415
9I1147LOOSE THERMAL9.3510
10J858LOOSE POSITIONAL0.235
10J858LOOSE THERMAL7.0710
11K738LOOSE POSITIONAL0.325
11K738LOOSE THERMAL10.1610
12L712LOOSE POSITIONAL0.225
12L712LOOSE THERMAL7.0910
13M618LOOSE POSITIONAL0.295
13M618LOOSE THERMAL10.1710
LS refinement shellResolution: 1.301→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 5557 -
Rwork0.351 110987 -
all-116544 -
obs--99.15 %
Refinement TLS params.

L33: 0.0002 °2 / T12: 0.0001 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.000100.00010-0-0.0002-0.0002-0.0003-0.00040-00.00010.00010.00020.0050.00010.0096-0.00010.001661.443306.81198.507
20.00060.00070.00030.00090.0003-0.0005-0.00040.0006-0.00080.00010.00070.00020.00020.00040.005600.00980.00020.0006126.101311.423194.549
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 513
2X-RAY DIFFRACTION1A515 - 825
3X-RAY DIFFRACTION1A1002 - 1830
4X-RAY DIFFRACTION1B1 - 227
5X-RAY DIFFRACTION1B228 - 805
6X-RAY DIFFRACTION1B1001 - 1806
7X-RAY DIFFRACTION1C4 - 261
8X-RAY DIFFRACTION1C262 - 827
9X-RAY DIFFRACTION1C1021 - 1827
10X-RAY DIFFRACTION1D4 - 146
11X-RAY DIFFRACTION1D1045 - 1333
12X-RAY DIFFRACTION1E7 - 108
13X-RAY DIFFRACTION1E811 - 815
14X-RAY DIFFRACTION1E1059 - 1815
15X-RAY DIFFRACTION1F3 - 93
16X-RAY DIFFRACTION1F99 - 819
17X-RAY DIFFRACTION1F1058 - 1819
18X-RAY DIFFRACTION1G12 - 83
19X-RAY DIFFRACTION1G86 - 821
20X-RAY DIFFRACTION1G1072 - 1821
21X-RAY DIFFRACTION1H11 - 85
22X-RAY DIFFRACTION1H1068 - 1358
23X-RAY DIFFRACTION1I3 - 72
24X-RAY DIFFRACTION1I1101 - 1360
25X-RAY DIFFRACTION1J1 - 56
26X-RAY DIFFRACTION1J61 - 732
27X-RAY DIFFRACTION1J1062 - 1261
28X-RAY DIFFRACTION1K6 - 54
29X-RAY DIFFRACTION1K1006 - 1315
30X-RAY DIFFRACTION1L3 - 46
31X-RAY DIFFRACTION1L747
32X-RAY DIFFRACTION1L1071 - 1514
33X-RAY DIFFRACTION1M1 - 40
34X-RAY DIFFRACTION1M746
35X-RAY DIFFRACTION1M1239 - 1332
36X-RAY DIFFRACTION2N1 - 513
37X-RAY DIFFRACTION2N515 - 829
38X-RAY DIFFRACTION2N2002 - 2830
39X-RAY DIFFRACTION2O1 - 227
40X-RAY DIFFRACTION2O228 - 805
41X-RAY DIFFRACTION2O2001 - 2806
42X-RAY DIFFRACTION2P4 - 261
43X-RAY DIFFRACTION2P262 - 827
44X-RAY DIFFRACTION2P2021 - 2827
45X-RAY DIFFRACTION2Q10 - 146
46X-RAY DIFFRACTION2Q2045 - 2333
47X-RAY DIFFRACTION2R7 - 108
48X-RAY DIFFRACTION2R811 - 815
49X-RAY DIFFRACTION2R2059 - 2815
50X-RAY DIFFRACTION2S3 - 93
51X-RAY DIFFRACTION2S99 - 819
52X-RAY DIFFRACTION2S2058 - 2819
53X-RAY DIFFRACTION2T12 - 83
54X-RAY DIFFRACTION2T86 - 821
55X-RAY DIFFRACTION2T1196 - 2821
56X-RAY DIFFRACTION2U11 - 85
57X-RAY DIFFRACTION2U2003 - 2358
58X-RAY DIFFRACTION2V3 - 72
59X-RAY DIFFRACTION2V2074 - 2322
60X-RAY DIFFRACTION2W1 - 56
61X-RAY DIFFRACTION2W61 - 732
62X-RAY DIFFRACTION2W2062 - 2261
63X-RAY DIFFRACTION2X6 - 54
64X-RAY DIFFRACTION2X2006 - 2315
65X-RAY DIFFRACTION2Y3 - 46
66X-RAY DIFFRACTION2Y747
67X-RAY DIFFRACTION2Y2071 - 2514
68X-RAY DIFFRACTION2Z1 - 40
69X-RAY DIFFRACTION2Z746
70X-RAY DIFFRACTION2Z2097 - 2332

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