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- PDB-5xdq: Bovine heart cytochrome c oxidase in the fully oxidized state wit... -

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Basic information

Entry
Database: PDB / ID: 5xdq
TitleBovine heart cytochrome c oxidase in the fully oxidized state with pH 7.3 at 1.77 angstrom resolution
Components(Cytochrome c oxidase subunit ...) x 13
KeywordsOXIDOREDUCTASE / proton pump / heme protein / respiratory chain
Function / homology
Function and homology information


Complex IV assembly / TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / Respiratory electron transport / respiratory chain complex IV / respiratory chain complex / cytochrome-c oxidase / oxidative phosphorylation ...Complex IV assembly / TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / Respiratory electron transport / respiratory chain complex IV / respiratory chain complex / cytochrome-c oxidase / oxidative phosphorylation / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / Mitochondrial protein degradation / ATP synthesis coupled electron transport / enzyme regulator activity / aerobic respiration / central nervous system development / respiratory electron transport chain / oxidoreductase activity / mitochondrial inner membrane / copper ion binding / heme binding / mitochondrion / metal ion binding
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 / Cytochrome C Oxidase; Chain J / Helix Hairpins - #90 / Cytochrome c oxidase, subunit 8 / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit 8 superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / : / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIc / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily / Cytochrome c oxidase, subunit VIIa superfamily / 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 VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit VIb / : / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase, subunit VIb superfamily / 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 2, C-terminal / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit Va / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit II / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / 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/quinol oxidase subunit II / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / 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 / Cupredoxin / Four Helix Bundle (Hemerythrin (Met), subunit A) / Few Secondary Structures / Irregular / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Helix Hairpins / Alpha Horseshoe / Arc Repressor Mutant, subunit A / Up-down Bundle / Immunoglobulin-like
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 (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsLuo, F.J. / Shimada, A. / Hagimoto, N. / Shimada, S. / Shinzawa-Itoh, K. / Yamashita, E. / Yoshikawa, S. / Tsukihara, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
JST CRESTJPMJCR12M3 Japan
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Structure of bovine cytochrome c oxidase crystallized at a neutral pH using a fluorinated detergent.
Authors: Luo, F. / Shinzawa-Itoh, K. / Hagimoto, K. / Shimada, A. / Shimada, S. / Yamashita, E. / Yoshikawa, S. / Tsukihara, T.
History
DepositionMar 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 15, 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.name
Revision 1.2Nov 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, 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)446,406140
Polymers409,31526
Non-polymers37,091114
Water51,9192882
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)223,79874
Polymers204,65713
Non-polymers19,14061
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)222,60866
Polymers204,65713
Non-polymers17,95153
Water23413
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)183.307, 205.904, 177.526
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(-0.993486, -0.00495, 0.113849), (0.001196, -0.999454, -0.033016), (0.11395, -0.032665, 0.992949)167.399139, 629.452332, 0.8313
3given(1), (1), (1)
4given(-0.99363, -0.000657, 0.112691), (-0.003434, -0.999342, -0.036102), (0.11264, -0.036259, 0.992974)166.157272, 630.581848, 2.24054
5given(1), (1), (1)
6given(-0.99351, -0.001553, 0.113734), (-0.002676, -0.999311, -0.037021), (0.113713, -0.037085, 0.992821)166.421265, 630.584045, 2.16003
7given(1), (1), (1)
8given(-0.993867, -0.007456, 0.110331), (0.004902, -0.999714, -0.023401), (0.110474, -0.022716, 0.993619)168.893692, 627.264465, -1.80005
9given(1), (1), (1)
10given(-0.991109, -0.047578, 0.124257), (0.043039, -0.998313, -0.038965), (0.125901, -0.03327, 0.991485)178.882965, 625.090393, -0.04686
11given(1), (1), (1)
12given(-0.99337, -0.006859, 0.114755), (0.003494, -0.999559, -0.0295), (0.114907, -0.028903, 0.992956)167.855209, 628.438721, -0.47776
13given(1), (1), (1)
14given(-0.993144, 0.001888, 0.11688), (-0.006493, -0.999217, -0.039033), (0.116715, -0.039524, 0.992379)164.649643, 631.317688, 2.5439
15given(1), (1), (1)
16given(-0.992426, -0.004428, 0.122763), (0.000578, -0.999507, -0.031384), (0.122841, -0.031075, 0.99194)165.643723, 629.388367, -0.48614
17given(1), (1), (1)
18given(-0.994704, -0.016475, 0.101457), (0.013892, -0.999563, -0.026113), (0.101842, -0.024565, 0.994497)173.449051, 626.590454, -0.43453
19given(1), (1), (1)
20given(-0.993959, -0.004854, 0.109647), (0.002618, -0.999786, -0.02053), (0.109723, -0.020119, 0.993759)168.299301, 626.571167, -2.27828
21given(1), (1), (1)
22given(-0.994126, 0.000986, 0.10822), (-0.003231, -0.999783, -0.020568), (0.108176, -0.020796, 0.993914)166.523422, 628.103638, -2.2284
23given(1), (1), (1)
24given(-0.993432, -0.025853, 0.111464), (0.022937, -0.999362, -0.02736), (0.1121, -0.024624, 0.993392)174.141693, 625.122437, -1.45011
25given(1), (1), (1)
26given(-0.993005, -0.019317, 0.116481), (0.016282, -0.999504, -0.026947), (0.116944, -0.024862, 0.992827)171.175537, 625.865967, -2.09451

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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 (domestic 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 (domestic 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 (domestic cattle) / References: UniProt: P00415
#4: Protein Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase subunit IV isform1 / Cytochrome c oxidase polypeptide IV / Cytochrome c ...Cytochrome c oxidase subunit IV isform1 / 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 (domestic 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 (domestic cattle) / References: UniProt: P00426
#6: Protein Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase polypeptide VIa / Cytochrome c oxidase polypeptide Vb


Mass: 10233.528 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic 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: 9629.782 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P07471
#8: Protein Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase polypeptide VII / Cytochrome c oxidase subunit AED / Cytochrome c oxidase ...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 (domestic 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 (domestic cattle) / References: UniProt: P04038
#10: Protein Cytochrome c oxidase subunit 7A1, mitochondrial / Cytochrome c oxidase subunit VIIIc / VIIIC / Cytochrome c oxidase subunit VIIa-heart / Cytochrome c ...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 (domestic cattle) / References: UniProt: P07470
#11: Protein Cytochrome c oxidase subunit 7B, mitochondrial / 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 (domestic cattle) / References: UniProt: P13183
#12: Protein/peptide Cytochrome c oxidase subunit 7C, mitochondrial / 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 (domestic cattle) / References: UniProt: P00430
#13: Protein/peptide Cytochrome c oxidase subunit 8B, mitochondrial / Cytochrome c oxidase polypeptide VIII-heart / Cytochrome c oxidase subunit 8-1 / Cytochrome c ...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 (domestic cattle) / References: UniProt: P10175

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Sugars , 1 types, 6 molecules

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


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 15 types, 2990 molecules

#14: Chemical
ChemComp-HEA / HEME-A


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


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


Mass: 749.007 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#19: Chemical ChemComp-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#20: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 56 / Source method: obtained synthetically / Formula: C2H6O2
#21: Chemical
ChemComp-TGL / TRISTEAROYLGLYCEROL / TRIACYLGLYCEROL


Mass: 891.480 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C57H110O6
#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


Mass: 759.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H81NO8P / Comment: phospholipid*YM
#24: Chemical
ChemComp-CHD / CHOLIC ACID


Mass: 408.571 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C24H40O5
#25: 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


Mass: 768.055 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C43H78NO8P / Comment: phospholipid*YM
#26: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#28: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 2882 / 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

Crystal growTemperature: 277 K / Method: batch mode / pH: 7.3
Details: 3% polythylene glycol (PEG), 0.35% decal maltose, 0.70% fluorinated octyl-maltoside, 33mM sodium acetate, 25mM Tris-HCL (pH 7.3)

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Data collection

DiffractionMean temperature: 50 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.77→200 Å / Num. obs: 643861 / % possible obs: 99.9 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.086 / Χ2: 1.869 / Net I/σ(I): 13 / Num. measured all: 5739764
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
1.77-1.798.2160391.6891100
1.79-1.88.2159971.6811000.944
1.8-1.828.4159931.68311000.901
1.82-1.838.4160681.69411000.86
1.83-1.858.4160101.68911000.788
1.85-1.878.5160031.70611000.699
1.87-1.898.5159931.711000.675
1.89-1.918.5159991.70911000.588
1.91-1.938.5160621.73511000.527
1.93-1.958.5160341.73211000.481
1.95-1.978.5160111.75811000.455
1.97-1.998.5160251.77611000.402
1.99-2.028.5160361.80311000.368
2.02-2.048.5160261.84311000.334
2.04-2.078.5160271.911000.3
2.07-2.18.5160661.92211000.272
2.1-2.138.5160271.94911000.256
2.13-2.168.6160381.98511000.23
2.16-2.198.6160601.99611000.205
2.19-2.238.6160561.97611000.186
2.23-2.278.6160211.948199.90.164
2.27-2.318.7161281.83811000.146
2.31-2.358.7160351.79611000.13
2.35-2.48.7161011.73911000.118
2.4-2.458.8160871.72211000.107
2.45-2.518.8160861.74411000.101
2.51-2.578.8161311.79411000.096
2.57-2.648.9161041.97711000.096
2.64-2.728.9160702.27111000.098
2.72-2.818.8161542.58199.90.099
2.81-2.918.8161272.5811000.092
2.91-3.039161452.493199.90.087
3.03-3.169.3161462.328199.80.086
3.16-3.339.4161442.108199.70.076
3.33-3.5410161911.885199.90.072
3.54-3.8111.6162191.817199.90.08
3.81-4.210.5162321.68199.60.067
4.2-4.810.1162031.54199.20.064
4.8-6.0511.2163821.585199.50.071
6.05-2009.4165851.475197.90.057

-
Processing

Software
NameVersionClassification
REFMAC5.8.0048refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V54

1v54


Resolution: 1.77→134.453 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 5.609 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1904 32361 5 %RANDOM
Rwork0.1639 ---
obs0.1652 611017 99.59 %-
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: 149.23 Å2 / Biso mean: 45.057 Å2 / Biso min: 6.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2--6.37 Å20 Å2
3----6.08 Å2
Refinement stepCycle: final / Resolution: 1.77→134.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28442 0 2542 2883 33867
Biso mean--69.38 66.25 -
Num. residues----3550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02232285
X-RAY DIFFRACTIONr_angle_refined_deg1.2032.02843368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.16453542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80523.0391247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76154922
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.60715126
X-RAY DIFFRACTIONr_chiral_restr0.0820.24591
X-RAY DIFFRACTIONr_gen_planes_refined0.020.02923134
X-RAY DIFFRACTIONr_rigid_bond_restr2.409331972
X-RAY DIFFRACTIONr_sphericity_free25.12158
X-RAY DIFFRACTIONr_sphericity_bonded23.645531034
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A4451LOOSE POSITIONAL0.235
1A4451LOOSE THERMAL5.9810
2B1885LOOSE POSITIONAL0.335
2B1885LOOSE THERMAL9.2110
3C2652LOOSE POSITIONAL0.555
3C2652LOOSE THERMAL5.4110
4D1190LOOSE POSITIONAL0.525
4D1190LOOSE THERMAL13.610
5E846LOOSE POSITIONAL0.225
5E846LOOSE THERMAL8.9610
6F717LOOSE POSITIONAL0.335
6F717LOOSE THERMAL6.3810
7G704LOOSE POSITIONAL0.345
7G704LOOSE THERMAL6.110
8H662LOOSE POSITIONAL0.275
8H662LOOSE THERMAL7.8410
9I601LOOSE POSITIONAL0.435
9I601LOOSE THERMAL10.9710
10J488LOOSE POSITIONAL0.475
10J488LOOSE THERMAL8.9910
11K379LOOSE POSITIONAL0.175
11K379LOOSE THERMAL11.0310
12L365LOOSE POSITIONAL0.455
12L365LOOSE THERMAL9.5110
13M330LOOSE POSITIONAL0.355
13M330LOOSE THERMAL10.910
LS refinement shellResolution: 1.77→1.816 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 2283 -
Rwork0.27 43922 -
all-46205 -
obs--97.42 %
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)
10.00150.002-0.00250.0034-0.00290.0066-0.0010.0007-0.0018-0.00050-0.00070.0004-0.00130.0010.08870.00110.00030.001800.116262.2971309.312197.9469
20.00490.00390.00240.00670.00390.008-0.00190.00170.0033-0.00220.00030.0021-0.00050.00130.00160.09430.00040.00060.0010.00150.1149126.3087314.1183194.2723
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 514
2X-RAY DIFFRACTION1A601 - 608
3X-RAY DIFFRACTION1B301
4X-RAY DIFFRACTION1C301
5X-RAY DIFFRACTION1D201
6X-RAY DIFFRACTION1L101
7X-RAY DIFFRACTION1M101
8X-RAY DIFFRACTION1B1 - 227
9X-RAY DIFFRACTION1B302
10X-RAY DIFFRACTION1E201
11X-RAY DIFFRACTION1C3 - 261
12X-RAY DIFFRACTION1A609
13X-RAY DIFFRACTION1C302 - 308
14X-RAY DIFFRACTION1G101
15X-RAY DIFFRACTION1T101
16X-RAY DIFFRACTION1D4 - 147
17X-RAY DIFFRACTION1E5 - 109
18X-RAY DIFFRACTION1F1 - 94
19X-RAY DIFFRACTION1F101
20X-RAY DIFFRACTION1G1 - 84
21X-RAY DIFFRACTION1G102
22X-RAY DIFFRACTION1H7 - 85
23X-RAY DIFFRACTION1I1 - 73
24X-RAY DIFFRACTION1J1 - 58
25X-RAY DIFFRACTION1J101
26X-RAY DIFFRACTION1K6 - 54
27X-RAY DIFFRACTION1L2 - 47
28X-RAY DIFFRACTION1M1 - 43
29X-RAY DIFFRACTION2N1 - 514
30X-RAY DIFFRACTION2N601 - 609
31X-RAY DIFFRACTION2O301
32X-RAY DIFFRACTION2P301
33X-RAY DIFFRACTION2Q201
34X-RAY DIFFRACTION2Z101
35X-RAY DIFFRACTION2O1 - 227
36X-RAY DIFFRACTION2O302 - 303
37X-RAY DIFFRACTION2P3 - 261
38X-RAY DIFFRACTION2G103
39X-RAY DIFFRACTION2N610
40X-RAY DIFFRACTION2P302 - 307
41X-RAY DIFFRACTION2T102 - 103
42X-RAY DIFFRACTION2Q4 - 147
43X-RAY DIFFRACTION2R5 - 109
44X-RAY DIFFRACTION2S1 - 94
45X-RAY DIFFRACTION2S101
46X-RAY DIFFRACTION2T1 - 84
47X-RAY DIFFRACTION2B303
48X-RAY DIFFRACTION2U7 - 85
49X-RAY DIFFRACTION2V1 - 73
50X-RAY DIFFRACTION2W1 - 58
51X-RAY DIFFRACTION2W101
52X-RAY DIFFRACTION2X6 - 54
53X-RAY DIFFRACTION2Y2 - 47
54X-RAY DIFFRACTION2Z1 - 43

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