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- PDB-5z85: The structure of azide-bound cytochrome c oxidase determined usin... -

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Basic information

Entry
Database: PDB / ID: 5z85
TitleThe structure of azide-bound cytochrome c oxidase determined using the another batch crystals exposed to 20 mM azide solution for 2 days
Components(Cytochrome c oxidase subunit ...) x 13
KeywordsOXIDOREDUCTASE / metalloenzyme cytochrome c oxidase proton pump bioenergetics heme copper / MEMBRANE PROTEIN
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; Chain F / Cytochrome c oxidase, subunit Vb / 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 ...Cytochrome C Oxidase; Chain F / Cytochrome c oxidase, subunit Vb / 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; Chain A / Cytochrome c oxidase-like, subunit I domain / : / 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
Similarity search - Domain/homology
AZIDE ION / CARDIOLIPIN / CHOLIC ACID / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / Chem-PEK / Chem-PGV / Chem-PSC / TRISTEAROYLGLYCEROL ...AZIDE ION / CARDIOLIPIN / CHOLIC ACID / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / Chem-PEK / 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: 1.85 Å
AuthorsShimada, A. / Hatano, K. / Tadehara, H. / Tsukihara, T.
Funding support Japan, 4items
OrganizationGrant numberCountry
JSPS KAKENHI15K18493 Japan
JSPS KAKENHI22370060 Japan
JSPS KAKENHI26291033 Japan
Japan Science and Technology Japan
CitationJournal: J. Biol. Chem. / Year: 2018
Title: X-ray structural analyses of azide-bound cytochromecoxidases reveal that the H-pathway is critically important for the proton-pumping activity.
Authors: Shimada, A. / Hatano, K. / Tadehara, H. / Yano, N. / Shinzawa-Itoh, K. / Yamashita, E. / Muramoto, K. / Tsukihara, T. / Yoshikawa, S.
History
DepositionJan 31, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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_ptnr1_label_alt_id / _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, mitochondrial
E: Cytochrome c oxidase subunit 5A, mitochondrial
F: Cytochrome c oxidase subunit 5B, mitochondrial
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, mitochondrial
K: Cytochrome c oxidase subunit 7B, mitochondrial
L: Cytochrome c oxidase subunit 7C, mitochondrial
M: Cytochrome c oxidase subunit 8B, mitochondrial
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, mitochondrial
R: Cytochrome c oxidase subunit 5A, mitochondrial
S: Cytochrome c oxidase subunit 5B, mitochondrial
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, mitochondrial
X: Cytochrome c oxidase subunit 7B, mitochondrial
Y: Cytochrome c oxidase subunit 7C, mitochondrial
Z: Cytochrome c oxidase subunit 8B, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)448,320155
Polymers410,21626
Non-polymers38,104129
Water29,1121616
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, mitochondrial
E: Cytochrome c oxidase subunit 5A, mitochondrial
F: Cytochrome c oxidase subunit 5B, mitochondrial
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, mitochondrial
K: Cytochrome c oxidase subunit 7B, mitochondrial
L: Cytochrome c oxidase subunit 7C, mitochondrial
M: Cytochrome c oxidase subunit 8B, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,31580
Polymers205,10813
Non-polymers19,20767
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, mitochondrial
R: Cytochrome c oxidase subunit 5A, mitochondrial
S: Cytochrome c oxidase subunit 5B, mitochondrial
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, mitochondrial
X: Cytochrome c oxidase subunit 7B, mitochondrial
Y: Cytochrome c oxidase subunit 7C, mitochondrial
Z: Cytochrome c oxidase subunit 8B, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,00575
Polymers205,10813
Non-polymers18,89762
Water23413
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)183.126, 205.893, 177.576
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(-0.993587, -0.00429, 0.112988), (-0.000119, -0.99924, -0.038981), (0.113069, -0.038744, 0.992831)167.315109, 630.793457, 2.84058
3given(1), (1), (1)
4given(-0.99388, 0.000363, 0.110461), (-0.005174, -0.99905, -0.04327), (0.110341, -0.043576, 0.992938)166.220169, 632.139465, 4.82506
5given(1), (1), (1)
6given(-0.993478, -0.001407, 0.114014), (-0.003669, -0.999012, -0.044294), (0.113964, -0.044423, 0.992491)166.211899, 632.12262, 4.46046
7given(1), (1), (1)
8given(-0.994377, 0.003262, 0.105849), (-0.005918, -0.999675, -0.024789), (0.105733, -0.025276, 0.994073)166.15184, 629.299377, -0.7013
9given(1), (1), (1)
10given(-0.991636, -0.048844, 0.119468), (0.043885, -0.998076, -0.043799), (0.121378, -0.03819, 0.991871)180.330551, 625.959595, 2.02298
11given(1), (1), (1)
12given(-0.993107, -0.008771, 0.116884), (0.003908, -0.99912, -0.041772), (0.117147, -0.041027, 0.992267)167.870758, 630.943665, 3.18518
13given(1), (1), (1)
14given(-0.993194, 0.006034, 0.116317), (-0.011013, -0.999048, -0.042212), (0.115952, -0.043206, 0.992315)163.53801, 632.474182, 4.07993
15given(1), (1), (1)
16given(-0.990711, -0.009786, 0.135632), (0.005166, -0.999396, -0.034371), (0.135887, -0.033351, 0.990163)165.05809, 629.727539, -0.87184
17given(1), (1), (1)
18given(-0.994854, -0.019536, 0.099416), (0.016385, -0.99934, -0.03242), (0.099984, -0.030624, 0.994518)174.84761, 627.441528, 1.6281
19given(1), (1), (1)
20given(-0.992851, 0.008977, 0.119025), (-0.015877, -0.998239, -0.057149), (0.118303, -0.058631, 0.991245)162.210342, 636.269531, 8.37875
21given(1), (1), (1)
22given(-0.994247, 0.00277, 0.107078), (-0.005606, -0.999641, -0.026191), (0.106967, -0.026641, 0.993906)166.164841, 629.591797, -0.3192
23given(1), (1), (1)
24given(-0.993432, -0.01955, 0.11274), (0.01604, -0.999361, -0.031958), (0.113293, -0.02994, 0.99311)171.92894, 626.955322, 0.07437
25given(1), (1), (1)
26given(-0.991982, -0.022269, 0.1244), (0.019108, -0.999465, -0.02655), (0.124925, -0.02396, 0.991877)170.207535, 625.30957, -3.56647

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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, mitochondrial / / 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, mitochondrial / / 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, mitochondrial / / 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, mitochondrial / / cytochrome c oxidase subunit 7 / Cytochrome c oxidase polypeptide VIa-heart / COXVIAH / Cytochrome ...cytochrome c oxidase subunit 7 / 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 subunit 9 / 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, mitochondrial / / 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, mitochondrial / / 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, mitochondrial / / Ccytochrome c oxidase subunit 12 / ytochrome c oxidase polypeptide VIIIA / Cytochrome c oxidase ...Ccytochrome c oxidase subunit 12 / ytochrome 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, mitochondrial / / 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, 8 molecules

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


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 16 types, 1737 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-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: N3
#19: Chemical
ChemComp-TGL / TRISTEAROYLGLYCEROL / TRIACYLGLYCEROL / Stearin


Mass: 891.480 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C57H110O6
#20: 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
#21: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 69 / Source method: obtained synthetically / Formula: C2H6O2
#22: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2
#23: 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
#24: Chemical
ChemComp-CHD / CHOLIC ACID / Cholic acid


Mass: 408.571 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H40O5
#26: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#27: 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
#28: 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
#29: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 1616 / 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: 4.08 Å3/Da / Density % sol: 69.86 % / Mosaicity: 0.129 °
Crystal growTemperature: 277 K / Method: batch mode / pH: 6.8 / Details: PEG4000, Sodium phosphate

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Data collection

DiffractionMean temperature: 50 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.85→200 Å / Num. obs: 561432 / % possible obs: 99.9 % / Redundancy: 15.8 % / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.032 / Rrim(I) all: 0.127 / Χ2: 2.32 / Net I/σ(I): 11.4 / Num. measured all: 8859305
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.8714.91.108140020.9210.2941.1471.716100
1.87-1.8814.91.083138880.9290.2871.1211.725100
1.88-1.914.90.987139320.9280.2611.0221.72100
1.9-1.9214.90.864139710.9490.2290.8941.771100
1.92-1.93150.801140200.9540.2120.8291.755100
1.93-1.95150.735138940.9630.1940.7611.79100
1.95-1.97150.703139510.9620.1860.7271.799100
1.97-1.9915.10.647139700.9660.1710.6691.824100
1.99-2.0115.10.595139040.9680.1570.6161.845100
2.01-2.0415.10.536139950.9770.1410.5541.89100
2.04-2.0615.10.505139540.9750.1330.5221.925100
2.06-2.0815.10.448139680.980.1180.4641.976100
2.08-2.1115.20.427139560.980.1130.4422.006100
2.11-2.1415.20.398140540.9820.1050.4122.039100
2.14-2.1615.20.356139110.9850.0940.3692.104100
2.16-2.1915.30.322139990.9870.0850.3332.131100
2.19-2.2215.30.298139540.9880.0780.3082.157100
2.22-2.2615.30.267139910.990.0710.2772.227100
2.26-2.2915.40.246139450.990.0650.2552.22100
2.29-2.3315.40.225139900.9920.0590.2322.23100
2.33-2.3715.40.207140260.9930.0550.2142.243100
2.37-2.4115.40.19139990.9930.050.1972.251100
2.41-2.4615.40.175140080.9940.0460.1812.292100
2.46-2.5115.40.164140450.9950.0430.172.355100
2.51-2.5715.40.152139930.9950.040.1572.397100
2.57-2.6315.40.145140320.9950.0380.152.485100
2.63-2.6915.30.14140430.9950.0370.1452.636100
2.69-2.7617.90.18140030.9950.0440.1852.684100
2.76-2.8417.80.173140650.9950.0420.1782.854100
2.84-2.9417.80.157140390.9960.0390.1622.913100
2.94-3.0417.70.145140650.9960.0360.1492.95100
3.04-3.1617.80.13140800.9960.0320.1342.938100
3.16-3.3117.80.118141260.9960.0290.1212.942100
3.31-3.4817.80.105141110.9970.0260.1082.923100
3.48-3.717.60.096141190.9970.0240.0992.925100
3.7-3.9916.90.087141710.9960.0220.092.91599.9
3.99-4.3915.60.078141550.9970.0210.0812.75599.9
4.39-5.0215.20.073142200.9970.020.0762.61299.7
5.02-6.3316.70.072143630.9960.0190.0752.47499.9
6.33-200140.066145200.9960.020.0692.33698.2

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0048refinement
PDB_EXTRACT3.24data extraction
REFMAC5.8.0048phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B1A

5b1a


Resolution: 1.85→40 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.495 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1887 28239 5 %RANDOM
Rwork0.1632 ---
obs0.1645 532947 99.3 %-
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: 164.19 Å2 / Biso mean: 40.336 Å2 / Biso min: 16.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2--3.22 Å20 Å2
3----3.45 Å2
Refinement stepCycle: final / Resolution: 1.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28506 0 2708 1618 32832
Biso mean--64.4 43.04 -
Num. residues----3558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.02332777
X-RAY DIFFRACTIONr_angle_refined_deg2.6452.03244145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.60653666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29822.9941249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.312154833
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.25415127
X-RAY DIFFRACTIONr_chiral_restr0.2180.24637
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.02223635
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A4568LOOSE POSITIONAL0.195
1A4568LOOSE THERMAL1.7710
2B1854LOOSE POSITIONAL0.395
2B1854LOOSE THERMAL4.3110
3C2680LOOSE POSITIONAL0.535
3C2680LOOSE THERMAL2.6910
4D1168LOOSE POSITIONAL0.755
4D1168LOOSE THERMAL7.0510
5E852LOOSE POSITIONAL0.35
5E852LOOSE THERMAL2.9910
6F756LOOSE POSITIONAL0.535
6F756LOOSE THERMAL3.8910
7G664LOOSE POSITIONAL0.645
7G664LOOSE THERMAL4.0310
8H662LOOSE POSITIONAL0.555
8H662LOOSE THERMAL3.4110
9I601LOOSE POSITIONAL0.445
9I601LOOSE THERMAL5.0810
10J460LOOSE POSITIONAL0.455
10J460LOOSE THERMAL2.710
11K377LOOSE POSITIONAL0.275
11K377LOOSE THERMAL2.6110
12L372LOOSE POSITIONAL0.435
12L372LOOSE THERMAL2.4610
13M335LOOSE POSITIONAL0.525
13M335LOOSE THERMAL3.1810
LS refinement shellResolution: 1.851→1.899 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 1855 -
Rwork0.231 36291 -
all-38146 -
obs--92.18 %
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)
10.239-0.0011-0.0960.1109-0.00060.27210.01430.03840.02940.00850.00490.0094-0.0137-0.0406-0.01920.05730.0101-0.01110.01020.00770.043964.938309.287198.122
20.33860.08190.06060.1771-0.00820.37390.02650.0822-0.09690.0350.0203-0.1063-0.0340.0728-0.04680.0454-0.0075-0.00660.0318-0.03830.1405126.3705314.3201194.3959
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 514
2X-RAY DIFFRACTION1A601 - 607
3X-RAY DIFFRACTION1A608 - 609
4X-RAY DIFFRACTION1C301
5X-RAY DIFFRACTION1D201
6X-RAY DIFFRACTION1M101 - 102
7X-RAY DIFFRACTION1T101
8X-RAY DIFFRACTION1B1 - 227
9X-RAY DIFFRACTION1B301 - 302
10X-RAY DIFFRACTION1C3 - 261
11X-RAY DIFFRACTION1C302 - 308
12X-RAY DIFFRACTION1G101 - 102
13X-RAY DIFFRACTION1T102
14X-RAY DIFFRACTION1D4 - 147
15X-RAY DIFFRACTION1E5 - 109
16X-RAY DIFFRACTION1F1 - 98
17X-RAY DIFFRACTION1F101
18X-RAY DIFFRACTION1G1 - 84
19X-RAY DIFFRACTION1H7 - 85
20X-RAY DIFFRACTION1I1 - 73
21X-RAY DIFFRACTION1J1 - 58
22X-RAY DIFFRACTION1K6 - 54
23X-RAY DIFFRACTION1L2 - 47
24X-RAY DIFFRACTION1M1 - 43
25X-RAY DIFFRACTION1A705 - 919
26X-RAY DIFFRACTION1B404 - 530
27X-RAY DIFFRACTION1C401 - 495
28X-RAY DIFFRACTION1D301 - 393
29X-RAY DIFFRACTION1E301 - 385
30X-RAY DIFFRACTION1F202 - 278
31X-RAY DIFFRACTION1G202 - 237
32X-RAY DIFFRACTION1H204 - 229
33X-RAY DIFFRACTION1I101 - 118
34X-RAY DIFFRACTION1J102 - 122
35X-RAY DIFFRACTION1K401 - 412
36X-RAY DIFFRACTION1L201 - 221
37X-RAY DIFFRACTION1M201 - 221
38X-RAY DIFFRACTION1N701 - 916
39X-RAY DIFFRACTION1O404 - 512
40X-RAY DIFFRACTION1P402 - 493
41X-RAY DIFFRACTION1Q304 - 348
42X-RAY DIFFRACTION1R304 - 346
43X-RAY DIFFRACTION1S204 - 264
44X-RAY DIFFRACTION1T202 - 232
45X-RAY DIFFRACTION1U205 - 233
46X-RAY DIFFRACTION1V201 - 214
47X-RAY DIFFRACTION1W102 - 113
48X-RAY DIFFRACTION1X101
49X-RAY DIFFRACTION1Y201 - 214
50X-RAY DIFFRACTION1Z204 - 212
51X-RAY DIFFRACTION1C309 - 310
52X-RAY DIFFRACTION1P310 - 311
53X-RAY DIFFRACTION2N1 - 514
54X-RAY DIFFRACTION2N601 - 607
55X-RAY DIFFRACTION2G103
56X-RAY DIFFRACTION2N608 - 610
57X-RAY DIFFRACTION2P301
58X-RAY DIFFRACTION2Q201
59X-RAY DIFFRACTION2Z101
60X-RAY DIFFRACTION2O1 - 227
61X-RAY DIFFRACTION2O301 - 302
62X-RAY DIFFRACTION2P3 - 261
63X-RAY DIFFRACTION2G104
64X-RAY DIFFRACTION2P302 - 309
65X-RAY DIFFRACTION2T103
66X-RAY DIFFRACTION2Q4 - 147
67X-RAY DIFFRACTION2R5 - 109
68X-RAY DIFFRACTION2S1 - 98
69X-RAY DIFFRACTION2S101
70X-RAY DIFFRACTION2T1 - 84
71X-RAY DIFFRACTION2U7 - 85
72X-RAY DIFFRACTION2V1 - 73
73X-RAY DIFFRACTION2W1 - 58
74X-RAY DIFFRACTION2X6 - 54
75X-RAY DIFFRACTION2Y2 - 47
76X-RAY DIFFRACTION2Z1 - 43

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