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- PDB-5zco: azide-bound cytochrome c oxidase structure determined using the c... -

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Basic information

Entry
Database: PDB / ID: 5zco
Titleazide-bound cytochrome c oxidase structure determined using the crystals exposed to 2 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: 1.9 Å
AuthorsShimada, A. / Hatano, K. / Tadehara, H. / Tsukihara, T.
Funding support Japan, 4items
OrganizationGrant numberCountry
JSPS KAKENHI15K18493 Japan
JSPS KAKENHI22370060 Japan
JSPS KAKENHI26291033 Japan
JST, CREST 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
DepositionFeb 19, 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_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_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)447,647133
Polymers410,21626
Non-polymers37,432107
Water30,0311667
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)223,75471
Polymers205,10813
Non-polymers18,64658
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)223,89462
Polymers205,10813
Non-polymers18,78649
Water23413
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)183.379, 206.655, 177.589
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(-0.993511, -0.003429, 0.113685), (-0.000585, -0.999378, -0.035255), (0.113735, -0.035093, 0.992891)167.083908, 632.494812, 1.66334
3given(1), (1), (1)
4given(-0.993559, 0.001265, 0.113311), (-0.005617, -0.999258, -0.038095), (0.113178, -0.038486, 0.992829)165.577499, 633.621826, 2.94756
5given(1), (1), (1)
6given(-0.993411, 0.0006, 0.114602), (-0.004916, -0.999289, -0.037377), (0.114498, -0.037694, 0.992708)165.681412, 633.365723, 2.36598
7given(1), (1), (1)
8given(-0.994537, 0.01334, 0.10353), (-0.015909, -0.999585, -0.024029), (0.103166, -0.025545, 0.994336)163.42807, 632.859375, 0.00245
9given(1), (1), (1)
10given(-0.99117, -0.049042, 0.123196), (0.044286, -0.998175, -0.041059), (0.124984, -0.035241, 0.991533)179.759598, 627.788696, 0.77926
11given(1), (1), (1)
12given(-0.992247, -0.010639, 0.123829), (0.005854, -0.999225, -0.038936), (0.124148, -0.037909, 0.991539)166.928192, 632.428284, 1.6022
13given(1), (1), (1)
14given(-0.993236, 0.006599, 0.115926), (-0.010911, -0.999271, -0.036596), (0.1156, -0.037614, 0.992583)163.54776, 633.774719, 2.35241
15given(1), (1), (1)
16given(-0.990878, -0.009689, 0.134413), (0.005263, -0.999433, -0.033247), (0.134659, -0.032236, 0.990367)165.381378, 631.738037, -1.0861
17given(1), (1), (1)
18given(-0.993692, -0.041057, 0.104363), (0.038435, -0.998896, -0.027014), (0.105357, -0.022832, 0.994172)181.434738, 625.628357, -1.45797
19given(1), (1), (1)
20given(-0.992206, 0.007884, 0.124356), (-0.013667, -0.998861, -0.045715), (0.123854, -0.047058, 0.991184)161.360565, 636.122314, 4.20309
21given(1), (1), (1)
22given(-0.994171, 0.004395, 0.107727), (-0.006774, -0.999741, -0.021725), (0.107603, -0.022328, 0.993943)165.690918, 631.258179, -1.7021
23given(1), (1), (1)
24given(-0.99342, -0.01346, 0.113735), (0.010274, -0.999539, -0.028554), (0.114067, -0.027198, 0.993101)170.08197, 629.545715, -0.81638
25given(1), (1), (1)
26given(-0.991429, -0.028524, 0.127496), (0.026257, -0.999467, -0.019424), (0.127982, -0.01591, 0.991649)171.637436, 625.061646, -6.40069

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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 / / 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, 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

#24: 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, 1766 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-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
#20: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 45 / Source method: obtained synthetically / Formula: C2H6O2
#21: Chemical
ChemComp-TGL / TRISTEAROYLGLYCEROL / TRIACYLGLYCEROL / Stearin


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


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


Num. of mol.: 2 / Source method: obtained synthetically
#26: 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
#27: 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
#28: 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
#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.: 1667 / 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: 4.1 Å3/Da / Density % sol: 70.01 % / Mosaicity: 0.182 °
Crystal growTemperature: 277 K / Method: batch mode / pH: 6.8 / Details: PEG 4000, 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: 1.9→200 Å / Num. obs: 523084 / % possible obs: 99.9 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.031 / Rrim(I) all: 0.116 / Χ2: 1.96 / Net I/σ(I): 12.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.9210.20.848130180.9330.2740.8921.726100
1.92-1.9310.30.811130390.9430.2610.8531.686100
1.93-1.9510.30.734129820.9520.2360.7721.692100
1.95-1.9710.40.697129630.9530.2240.7331.712100
1.97-1.9910.40.637130520.9570.2050.671.722100
1.99-2.0110.40.582129630.9580.1870.6121.739100
2.01-2.0310.40.523130400.9670.1680.551.77100
2.03-2.0510.50.492130230.9690.1580.5171.778100
2.05-2.0710.50.443129380.9740.1420.4651.832100
2.07-2.0910.60.406131140.9760.130.4261.832100
2.09-2.1110.60.38129330.9770.1210.41.842100
2.11-2.1410.60.357130450.9790.1140.3751.862100
2.14-2.1710.70.318130130.9830.1020.3351.89100
2.17-2.1910.70.287130510.9850.0920.3011.908100
2.19-2.2210.70.264130180.9870.0840.2771.892100
2.22-2.2510.70.24130060.9890.0760.2521.972100
2.25-2.2810.80.214130390.990.0680.2251.881100
2.28-2.3210.90.193130660.9920.0610.2021.813100
2.32-2.36110.177129930.9930.0560.1851.79100
2.36-2.39110.161130890.9940.0510.1691.766100
2.39-2.4411.10.147130390.9950.0460.1541.75100
2.44-2.4811.10.137130470.9950.0430.1441.783100
2.48-2.5311.20.126130500.9960.040.1331.779100
2.53-2.5811.20.119131100.9960.0380.1251.825100
2.58-2.6311.30.115130170.9950.0360.121.91100
2.63-2.711.30.113131110.9950.0360.1192.07100
2.7-2.7616.70.245130330.9950.0620.2532.089100
2.76-2.84170.232131050.9950.0590.242.248100
2.84-2.92170.208130960.9950.0520.2152.267100
2.92-3.02170.183131070.9960.0460.1882.284100
3.02-3.1217.20.162131280.9960.0410.1672.247100
3.12-3.2517.30.14131170.9960.0350.1442.197100
3.25-3.417.50.121131690.9970.030.1242.134100
3.4-3.5817.60.106131390.9970.0260.1092.166100
3.58-3.8170.094131720.9970.0240.0972.19699.9
3.8-4.0915.50.082131380.9960.0220.0852.14799.5
4.09-4.5113.70.07130830.9970.020.0731.91698.8
4.51-5.1613.20.07131810.9960.0210.0731.95599.1
5.16-6.515.20.069133720.9970.0190.0721.86199.8
6.5-20012.20.062134850.9970.0210.0661.93197.6

-
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: 1.9→40 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.768 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1892 26411 5.1 %RANDOM
Rwork0.164 ---
obs0.1653 496443 99.65 %-
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: 164.03 Å2 / Biso mean: 42.928 Å2 / Biso min: 17.82 Å2
Baniso -1Baniso -2Baniso -3
1-2.04 Å20 Å20 Å2
2--1.84 Å20 Å2
3----3.88 Å2
Refinement stepCycle: final / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28506 0 2676 1674 32856
Biso mean--67.66 47.08 -
Num. residues----3558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.02332974
X-RAY DIFFRACTIONr_angle_refined_deg2.5832.03344498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58953706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3522.9571258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.182154873
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.08815131
X-RAY DIFFRACTIONr_chiral_restr0.2120.24684
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.02223851
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A4647LOOSE POSITIONAL0.215
1A4647LOOSE THERMAL1.7210
2B1895LOOSE POSITIONAL0.415
2B1895LOOSE THERMAL4.1910
3C2708LOOSE POSITIONAL0.495
3C2708LOOSE THERMAL2.9410
4D1215LOOSE POSITIONAL0.925
4D1215LOOSE THERMAL7.9410
5E841LOOSE POSITIONAL0.35
5E841LOOSE THERMAL3.2310
6F749LOOSE POSITIONAL0.735
6F749LOOSE THERMAL4.2110
7G686LOOSE POSITIONAL0.665
7G686LOOSE THERMAL3.7910
8H662LOOSE POSITIONAL0.345
8H662LOOSE THERMAL3.5310
9I601LOOSE POSITIONAL0.65
9I601LOOSE THERMAL5.2210
10J451LOOSE POSITIONAL0.685
10J451LOOSE THERMAL2.4910
11K377LOOSE POSITIONAL0.265
11K377LOOSE THERMAL2.9210
12L372LOOSE POSITIONAL0.415
12L372LOOSE THERMAL3.3110
13M335LOOSE POSITIONAL0.695
13M335LOOSE THERMAL3.1910
LS refinement shellResolution: 1.901→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 1896 -
Rwork0.218 35902 -
all-37798 -
obs--98.07 %
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)
10.2008-0.0039-0.09120.093-0.00090.23210.010.03360.02470.0080.00680.0086-0.0069-0.042-0.01680.01340.004-0.01070.04660.00940.055462.6382310.3653197.9354
20.27040.07570.05070.1671-0.00110.34340.02470.0738-0.09890.02480.0221-0.1163-0.03160.0696-0.04690.0102-0.0041-0.00990.0405-0.04290.1572126.4382315.4949194.4202
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 DIFFRACTION1B301 - 302
5X-RAY DIFFRACTION1C301
6X-RAY DIFFRACTION1D201
7X-RAY DIFFRACTION1M101
8X-RAY DIFFRACTION1B1 - 227
9X-RAY DIFFRACTION1B303
10X-RAY DIFFRACTION1E201
11X-RAY DIFFRACTION1C3 - 261
12X-RAY DIFFRACTION1C302 - 309
13X-RAY DIFFRACTION1G101
14X-RAY DIFFRACTION1N601
15X-RAY DIFFRACTION1D4 - 147
16X-RAY DIFFRACTION1E5 - 109
17X-RAY DIFFRACTION1F1 - 98
18X-RAY DIFFRACTION1F101
19X-RAY DIFFRACTION1G1 - 84
20X-RAY DIFFRACTION1H7 - 85
21X-RAY DIFFRACTION1I1 - 73
22X-RAY DIFFRACTION1J1 - 58
23X-RAY DIFFRACTION1K6 - 54
24X-RAY DIFFRACTION1L2 - 47
25X-RAY DIFFRACTION1M1 - 43
26X-RAY DIFFRACTION1A707 - 934
27X-RAY DIFFRACTION1B402 - 553
28X-RAY DIFFRACTION1C402 - 500
29X-RAY DIFFRACTION1D315 - 418
30X-RAY DIFFRACTION1E316 - 370
31X-RAY DIFFRACTION1F204 - 279
32X-RAY DIFFRACTION1G202 - 240
33X-RAY DIFFRACTION1H101 - 143
34X-RAY DIFFRACTION1I107 - 127
35X-RAY DIFFRACTION1J202 - 210
36X-RAY DIFFRACTION1K104 - 119
37X-RAY DIFFRACTION1L202 - 219
38X-RAY DIFFRACTION1M207 - 223
39X-RAY DIFFRACTION1C310 - 311
40X-RAY DIFFRACTION1P308 - 309
41X-RAY DIFFRACTION2N1 - 514
42X-RAY DIFFRACTION2N602 - 608
43X-RAY DIFFRACTION2G102
44X-RAY DIFFRACTION2N609 - 610
45X-RAY DIFFRACTION2P301
46X-RAY DIFFRACTION2Q201
47X-RAY DIFFRACTION2Z101 - 102
48X-RAY DIFFRACTION2O1 - 227
49X-RAY DIFFRACTION2O301 - 302
50X-RAY DIFFRACTION2P3 - 261
51X-RAY DIFFRACTION2G103
52X-RAY DIFFRACTION2P303 - 307
53X-RAY DIFFRACTION2T101 - 102
54X-RAY DIFFRACTION2U101
55X-RAY DIFFRACTION2Q4 - 147
56X-RAY DIFFRACTION2R5 - 109
57X-RAY DIFFRACTION2S1 - 98
58X-RAY DIFFRACTION2S101
59X-RAY DIFFRACTION2T1 - 84
60X-RAY DIFFRACTION2U7 - 85
61X-RAY DIFFRACTION2V1 - 73
62X-RAY DIFFRACTION2W1 - 58
63X-RAY DIFFRACTION2X6 - 54
64X-RAY DIFFRACTION2Y2 - 47
65X-RAY DIFFRACTION2Z1 - 43
66X-RAY DIFFRACTION2N702 - 906
67X-RAY DIFFRACTION2O402 - 499
68X-RAY DIFFRACTION2P402 - 488
69X-RAY DIFFRACTION2Q302 - 329
70X-RAY DIFFRACTION2R304 - 338
71X-RAY DIFFRACTION2S201 - 244
72X-RAY DIFFRACTION2T203 - 236
73X-RAY DIFFRACTION2U201 - 231
74X-RAY DIFFRACTION2V101 - 111
75X-RAY DIFFRACTION2W201 - 205
76X-RAY DIFFRACTION2X102 - 112
77X-RAY DIFFRACTION2Y203 - 210
78X-RAY DIFFRACTION2Z201 - 205

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