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- PDB-6j8m: Low-dose structure of bovine heart cytochrome c oxidase in the fu... -

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Basic information

Entry
Database: PDB / ID: 6j8m
TitleLow-dose structure of bovine heart cytochrome c oxidase in the fully oxidized state determined using 30 keV X-ray
Components(Cytochrome c oxidase subunit ...) x 13
KeywordsOXIDOREDUCTASE / proton pump / heme / respiratory chain
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 VIb / Cytochrome C Oxidase; Chain D / Cytochrome c oxidase subunit IV / Cytochrome C Oxidase; Chain K / Cytochrome C Oxidase, chain K / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit VIIa / Cytochrome C Oxidase; Chain I / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome C Oxidase; Chain G ...Cytochrome c oxidase, subunit VIb / Cytochrome C Oxidase; Chain D / Cytochrome c oxidase subunit IV / Cytochrome C Oxidase; Chain K / Cytochrome C Oxidase, chain K / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit VIIa / Cytochrome C Oxidase; Chain I / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome C Oxidase; Chain G / Cytochrome c oxidase, subunit VIa / Cytochrome C Oxidase; Chain M / Cytochrome C Oxidase; Chain L / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit III, four-helix bundle / Helix Hairpins - #90 / Cytochrome C Oxidase; Chain J / 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. / Helix Hairpins - #70 / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Cupredoxins - blue copper proteins / Four Helix Bundle (Hemerythrin (Met), subunit A) / Cupredoxin / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Few Secondary Structures / Irregular / Alpha Horseshoe / Helix Hairpins / Arc Repressor Mutant, subunit A / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
CARDIOLIPIN / CHOLIC ACID / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / Chem-PEK / PEROXIDE ION / Chem-PGV / Chem-PSC / TRISTEAROYLGLYCEROL ...CARDIOLIPIN / CHOLIC ACID / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / Chem-PEK / PEROXIDE ION / Chem-PGV / Chem-PSC / TRISTEAROYLGLYCEROL / 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: 1.9 Å
AuthorsUeno, G. / Shimada, A. / Yamashita, E. / Hasegawa, K. / Kumasaka, T. / Shinzawa-Itoh, K. / Yoshikawa, S. / Tsukihara, T. / Yamamoto, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
Japan Science and Technology Japan
CitationJournal: J.Synchrotron Radiat. / Year: 2019
Title: Low-dose X-ray structure analysis of cytochrome c oxidase utilizing high-energy X-rays.
Authors: Ueno, G. / Shimada, A. / Yamashita, E. / Hasegawa, K. / Kumasaka, T. / Shinzawa-Itoh, K. / Yoshikawa, S. / Tsukihara, T. / Yamamoto, M.
History
DepositionJan 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 4, 2019Group: Data collection / Category: reflns_shell
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.d_res_high ..._reflns_shell.Rmerge_I_obs / _reflns_shell.d_res_high / _reflns_shell.d_res_low / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rrim_I_all / _reflns_shell.pdbx_redundancy / _reflns_shell.percent_possible_all
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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
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
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
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
Z: Cytochrome c oxidase subunit 8B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)442,86682
Polymers410,21626
Non-polymers32,65056
Water46,0822558
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
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
M: Cytochrome c oxidase subunit 8B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,43341
Polymers205,10813
Non-polymers16,32528
Water23413
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
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
Z: Cytochrome c oxidase subunit 8B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,43341
Polymers205,10813
Non-polymers16,32528
Water23413
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)182.020, 203.540, 177.410
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 - 229
2126O1 - 229
1136C1 - 272
2136P1 - 272
1146D4 - 147
2146Q4 - 147
1156E5 - 109
2156R5 - 109
1166F1 - 99
2166S1 - 99
1176G1 - 85
2176T1 - 85
1186H7 - 85
2186U7 - 85
1196I1 - 73
2196V1 - 73
11106J1 - 59
21106W1 - 59
11116K6 - 54
21116X6 - 54
11126L2 - 47
21126Y2 - 47
11136M1 - 43
21136Z1 - 43

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

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.993106, -0.005399, 0.117098), (4.9E-5, -0.998958, -0.045639), (0.117223, -0.045318, 0.992071)165.871902, 624.762329, 4.53737
3given(1), (1), (1)
4given(-0.993288, 0.000221, 0.115666), (-0.006028, -0.998738, -0.049861), (0.115509, -0.050224, 0.992036)164.291885, 626.212036, 6.43666
5given(1), (1), (1)
6given(-0.993015, -0.001746, 0.117977), (-0.003779, -0.998907, -0.046589), (0.117929, -0.046709, 0.991923)164.569565, 625.356689, 4.90245
7given(1), (1), (1)
8given(-0.993699, -0.002505, 0.112051), (-0.001677, -0.999306, -0.037216), (0.112066, -0.03717, 0.993005)165.895386, 623.58606, 2.70824
9given(1), (1), (1)
10given(-0.990621, -0.057936, 0.123747), (0.051877, -0.997317, -0.051642), (0.126407, -0.044738, 0.990969)181.3367, 618.85437, 3.57102
11given(1), (1), (1)
12given(-0.993749, -0.007419, 0.111391), (0.00322, -0.999279, -0.037829), (0.111591, -0.037234, 0.993056)167.929031, 622.792053, 2.47127
13given(1), (1), (1)
14given(-0.992611, 0.00095, 0.121333), (-0.007608, -0.998489, -0.054416), (0.121098, -0.054937, 0.991119)163.066742, 627.028748, 7.06681
15given(1), (1), (1)
16given(-0.991611, -0.002056, 0.129238), (-0.003333, -0.999134, -0.041464), (0.129211, -0.041547, 0.990746)162.649582, 624.744629, 2.39382
17given(1), (1), (1)
18given(-0.992893, -0.04829, 0.108771), (0.044876, -0.998427, -0.033624), (0.110224, -0.028503, 0.993498)181.588257, 616.452759, -0.30702
19given(1), (1), (1)
20given(-0.992772, 0.002678, 0.119982), (-0.008308, -0.998886, -0.046453), (0.119724, -0.047115, 0.991689)162.887909, 625.813843, 4.91097
21given(1), (1), (1)
22given(-0.993515, 0.000603, 0.113699), (-0.004314, -0.999466, -0.032397), (0.113619, -0.032677, 0.992987)164.573257, 623.307739, 0.94022
23given(1), (1), (1)
24given(-0.99271, -0.012484, 0.119883), (0.007006, -0.998916, -0.046014), (0.120328, -0.044839, 0.991721)167.350906, 623.83551, 4.0068
25given(1), (1), (1)
26given(-0.991813, -0.019744, 0.12616), (0.014321, -0.99894, -0.043749), (0.12689, -0.041584, 0.991045)168.10022, 622.141785, 1.96965

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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 natural source / Source: (natural) 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 natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P68530
#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 natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00415
#4: Protein Cytochrome c oxidase subunit 4 isoform 1 / / Cytochrome c oxidase polypeptide IV / Cytochrome c oxidase subunit IV isoform 1 / COX IV-1


Mass: 17179.646 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) 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 natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00426
#6: Protein Cytochrome c oxidase subunit 5B / / cytochrome c oxidase subunit 6 / Cytochrome c oxidase polypeptide VIa / Cytochrome c oxidase polypeptide Vb


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


Mass: 9629.782 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07471
#8: Protein Cytochrome c oxidase subunit 6B1 / / cytochrome c oxidase subunit 8 / Cytochrome c oxidase polypeptide VII / Cytochrome c oxidase ...cytochrome c oxidase subunit 8 / Cytochrome c oxidase polypeptide VII / Cytochrome c oxidase subunit AED / Cytochrome c oxidase subunit VIb isoform 1 / COX VIb-1


Mass: 10039.244 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00429
#9: Protein Cytochrome c oxidase subunit 6C / / Cytochrome c oxidase polypeptide VIc / Cytochrome c oxidase subunit STA


Mass: 8537.019 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P04038
#10: Protein Cytochrome c oxidase subunit 7A1 / / cytochrome c oxidase subunit 10 / Cytochrome c oxidase subunit VIIIc / VIIIC / Cytochrome c oxidase ...cytochrome c oxidase subunit 10 / Cytochrome c oxidase subunit VIIIc / VIIIC / Cytochrome c oxidase subunit VIIa-heart / Cytochrome c oxidase subunit VIIa-H / Cytochrome c oxidase subunit VIIa-muscle / Cytochrome c oxidase subunit VIIa-M


Mass: 6682.726 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07470
#11: Protein Cytochrome c oxidase subunit 7B / / cytochrome c oxidase subunit 11 / Cytochrome c oxidase polypeptide VIIb / IHQ


Mass: 6365.217 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13183
#12: Protein/peptide Cytochrome c oxidase subunit 7C / / cytochrome c oxidase subunit 12 / Cytochrome c oxidase polypeptide VIIIA / Cytochrome c oxidase ...cytochrome c oxidase subunit 12 / Cytochrome c oxidase polypeptide VIIIA / Cytochrome c oxidase polypeptide VIIc


Mass: 5449.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00430
#13: Protein/peptide Cytochrome c oxidase subunit 8B / / cytochrome c oxidase subunit 13 / Cytochrome c oxidase polypeptide VIII-heart / Cytochrome c ...cytochrome c oxidase subunit 13 / Cytochrome c oxidase polypeptide VIII-heart / Cytochrome c oxidase subunit 8-1 / Cytochrome c oxidase subunit 8H / IX / VIIIb


Mass: 4967.756 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P10175

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Sugars , 1 types, 4 molecules

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


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 14 types, 2610 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.: 4 / Source method: obtained synthetically / Formula: Na
#18: 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.: 8 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#19: Chemical ChemComp-PER / PEROXIDE ION / Peroxide


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#20: Chemical
ChemComp-TGL / TRISTEAROYLGLYCEROL / TRIACYLGLYCEROL / Stearin


Mass: 891.480 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C57H110O6
#21: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2
#22: Chemical
ChemComp-CHD / CHOLIC ACID / Cholic acid


Mass: 408.571 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C24H40O5
#23: 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.: 6 / Source method: obtained synthetically / Formula: C43H78NO8P / Comment: phospholipid*YM
#24: 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.: 4 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#26: Chemical ChemComp-PSC / (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE / PHOSPHATIDYLCHOLINE / 2-LINOLEOYL-1-PALMITOYL-SN-GYCEROL-3-PHOSPHOCHOLINE / Phosphatidylcholine


Mass: 759.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H81NO8P / Comment: phospholipid*YM
#27: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#28: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2558 / Source method: isolated from a natural source / Formula: H2O

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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

CrystalDensity Matthews: 4.01 Å3/Da / Density % sol: 69.3 %
Crystal growTemperature: 277 K / Method: batch mode / pH: 5.8 / Details: PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.4133 Å
DetectorType: DECTRIS PILATUS3 X CdTe 300K / Detector: PIXEL / Date: Jun 8, 2016 / Details: Undulator 3rd harmonic, Compound refractive lends
RadiationMonochromator: Si (111) double crystal monochraomator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.4133 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 503312 / % possible obs: 98.09 % / Redundancy: 4.9 % / Biso Wilson estimate: 38.511 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.047 / Rrim(I) all: 0.11 / Χ2: 1.153 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.974.230.9731.4490480.6970.5351.11696.33
1.97-2.054.40.7111.9494260.8010.3830.81196.87
2.05-2.144.560.5342.6498460.8670.2810.60797.68
2.14-2.254.720.4013.5501370.9050.2070.45398.23
2.25-2.394.740.3014.7504480.940.1560.34198.64
2.39-2.584.740.2326503670.9610.1190.26198.53
2.58-2.844.610.1698505470.9710.0880.19198.65
2.84-3.254.390.10311.5497200.9840.0540.11796.76
3.25-4.095.490.07717.1512510.9920.0360.08599.32
4.09-406.980.06523.3525220.9940.0260.0799.87

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0048refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
REFMAC5.8.0048phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B1B

5b1b


Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 6.226 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.103 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1992 25030 5 %RANDOM
Rwork0.1721 ---
obs0.1735 478268 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 163.32 Å2 / Biso mean: 42.87 Å2 / Biso min: 15.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20 Å2
2--0.86 Å20 Å2
3----1.28 Å2
Refinement stepCycle: final / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28506 0 2234 2558 33298
Biso mean--69.88 51.61 -
Num. residues----3558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0232334
X-RAY DIFFRACTIONr_angle_refined_deg1.6592.01843763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92153669
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22622.9821254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01154830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.13915128
X-RAY DIFFRACTIONr_chiral_restr0.1090.24618
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02123481
X-RAY DIFFRACTIONr_rigid_bond_restr4.57132
X-RAY DIFFRACTIONr_sphericity_bonded5.461512
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A4232LOOSE POSITIONAL0.215
1A4232LOOSE THERMAL1.7710
2B1872LOOSE POSITIONAL0.375
2B1872LOOSE THERMAL3.3610
3C2646LOOSE POSITIONAL0.45
3C2646LOOSE THERMAL1.9510
4D1157LOOSE POSITIONAL0.65
4D1157LOOSE THERMAL8.8210
5E841LOOSE POSITIONAL0.285
5E841LOOSE THERMAL2.7410
6F701LOOSE POSITIONAL0.485
6F701LOOSE THERMAL3.3410
7G633LOOSE POSITIONAL0.395
7G633LOOSE THERMAL2.4210
8H662LOOSE POSITIONAL0.55
8H662LOOSE THERMAL2.310
9I593LOOSE POSITIONAL0.745
9I593LOOSE THERMAL3.1510
10J460LOOSE POSITIONAL0.365
10J460LOOSE THERMAL1.8910
11K391LOOSE POSITIONAL0.235
11K391LOOSE THERMAL2.1210
12L380LOOSE POSITIONAL0.365
12L380LOOSE THERMAL1.9510
13M335LOOSE POSITIONAL0.375
13M335LOOSE THERMAL2.210
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 1768 -
Rwork0.302 34518 -
all-36286 -
obs--96.23 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2052-0.0054-0.08450.11720.00160.26270.02230.04760.02530.00420.00080.0150.0015-0.0434-0.02310.00340.0120.00290.22370.00990.00662.008305.719197.85
20.33040.07180.06890.1936-0.01420.40060.03230.1177-0.07810.01740.0219-0.081-0.02930.0925-0.05420.00690.0023-0.0070.2345-0.03380.0476125.679310.523194.1
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 514
2X-RAY DIFFRACTION1A601 - 607
3X-RAY DIFFRACTION1B301
4X-RAY DIFFRACTION1M101
5X-RAY DIFFRACTION1B1 - 227
6X-RAY DIFFRACTION1B302
7X-RAY DIFFRACTION1E201
8X-RAY DIFFRACTION1C3 - 261
9X-RAY DIFFRACTION1A608
10X-RAY DIFFRACTION1C301 - 307
11X-RAY DIFFRACTION1G101
12X-RAY DIFFRACTION1T101
13X-RAY DIFFRACTION1D4 - 147
14X-RAY DIFFRACTION1E5 - 109
15X-RAY DIFFRACTION1F1 - 98
16X-RAY DIFFRACTION1F101
17X-RAY DIFFRACTION1G1 - 84
18X-RAY DIFFRACTION1H7 - 85
19X-RAY DIFFRACTION1I1 - 73
20X-RAY DIFFRACTION1J1 - 58
21X-RAY DIFFRACTION1K6 - 54
22X-RAY DIFFRACTION1L2 - 47
23X-RAY DIFFRACTION1M1 - 43
24X-RAY DIFFRACTION1A707 - 962
25X-RAY DIFFRACTION1B404 - 592
26X-RAY DIFFRACTION1C401 - 523
27X-RAY DIFFRACTION1D301 - 441
28X-RAY DIFFRACTION1E301 - 389
29X-RAY DIFFRACTION1F211 - 288
30X-RAY DIFFRACTION1G201 - 249
31X-RAY DIFFRACTION1H168
32X-RAY DIFFRACTION1K130 - 144
33X-RAY DIFFRACTION1L205 - 236
34X-RAY DIFFRACTION1N706 - 963
35X-RAY DIFFRACTION1O402 - 419
36X-RAY DIFFRACTION1P402 - 513
37X-RAY DIFFRACTION1R354 - 382
38X-RAY DIFFRACTION1S211 - 309
39X-RAY DIFFRACTION1T240
40X-RAY DIFFRACTION1U155
41X-RAY DIFFRACTION1V136
42X-RAY DIFFRACTION1X101
43X-RAY DIFFRACTION2N1 - 514
44X-RAY DIFFRACTION2N601 - 607
45X-RAY DIFFRACTION2Z101
46X-RAY DIFFRACTION2O1 - 227
47X-RAY DIFFRACTION2O302
48X-RAY DIFFRACTION2R201
49X-RAY DIFFRACTION2P3 - 261
50X-RAY DIFFRACTION2G102
51X-RAY DIFFRACTION2N609
52X-RAY DIFFRACTION2P301 - 305
53X-RAY DIFFRACTION2T102 - 103
54X-RAY DIFFRACTION2Q4 - 147
55X-RAY DIFFRACTION2R5 - 109
56X-RAY DIFFRACTION2S1 - 98
57X-RAY DIFFRACTION2S101
58X-RAY DIFFRACTION2T1 - 84
59X-RAY DIFFRACTION2U7 - 85
60X-RAY DIFFRACTION2V1 - 73
61X-RAY DIFFRACTION2W1 - 58
62X-RAY DIFFRACTION2X6 - 54
63X-RAY DIFFRACTION2Y2 - 47
64X-RAY DIFFRACTION2Z1 - 43
65X-RAY DIFFRACTION2B401 - 403

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