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- PDB-3x2q: X-ray structure of cyanide-bound bovine heart cytochrome c oxidas... -

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Basic information

Entry
Database: PDB / ID: 3x2q
TitleX-ray structure of cyanide-bound bovine heart cytochrome c oxidase in the fully oxidized state at 2.0 angstrom resolution
Components(Cytochrome c oxidase subunit ...) x 13
KeywordsOXIDOREDUCTASE / respiratory chain / electron transport / heme / iron / mitochondorial inner membrane
Function / homology
Function and homology information


TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / : / regulation of oxidative phosphorylation / Respiratory electron transport / cytochrome-c oxidase / : ...TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / : / regulation of oxidative phosphorylation / Respiratory electron transport / cytochrome-c oxidase / : / oxidative phosphorylation / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / Mitochondrial protein degradation / electron transport coupled proton transport / ATP synthesis coupled electron transport / enzyme regulator activity / central nervous system development / mitochondrial inner membrane / oxidoreductase activity / 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 / Helix Hairpins - #90 / Cytochrome C Oxidase; Chain J / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit 8 superfamily / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit VIIa superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / Cytochrome c oxidase subunit VIc / Cytochrome C oxidase chain VIIB / : / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase subunit Va / Cytochrome c oxidase, subunit VIb / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase subunit I domain / Cytochrome c oxidase, subunit II / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Helix Hairpins - #70 / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Cupredoxins - blue copper proteins / Four Helix Bundle (Hemerythrin (Met), subunit A) / Cupredoxin / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Few Secondary Structures / Irregular / Alpha Horseshoe / Helix Hairpins / Arc Repressor Mutant, subunit A / Up-down Bundle / Immunoglobulin-like / Sandwich
Similarity search - Domain/homology
CARDIOLIPIN / CHOLIC ACID / COPPER (II) ION / DINUCLEAR COPPER ION / CYANIDE ION / HEME-A / Chem-PEK / Chem-PGV / Chem-PSC / TRISTEAROYLGLYCEROL ...CARDIOLIPIN / CHOLIC ACID / COPPER (II) ION / DINUCLEAR COPPER ION / CYANIDE 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: 2 Å
AuthorsYano, N. / Muramoto, K. / Mochizuki, M. / Shinzawa-Itoh, K. / Yamashita, E. / Yoshikawa, S. / Tsukihara, T.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: X-ray structure of cyanide-bound bovine heart cytochrome c oxidase in the fully oxidized state at 2.0 angstrom resolution.
Authors: Yano, N. / Muramoto, K. / Mochizuki, M. / Shinzawa-Itoh, K. / Yamashita, E. / Yoshikawa, S. / Tsukihara, T.
History
DepositionDec 26, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 10, 2021Group: Advisory / Derived calculations / Structure summary
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._chem_comp.pdbx_synonyms / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_validate_chiral
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c oxidase subunit 1
B: Cytochrome c oxidase subunit 2
C: Cytochrome c oxidase subunit 3
D: Cytochrome c oxidase subunit 4 isoform 1, 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)441,99180
Polymers410,21626
Non-polymers31,77554
Water23,1671286
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)220,99540
Polymers205,10813
Non-polymers15,88827
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)220,99540
Polymers205,10813
Non-polymers15,88827
Water23413
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)183.678, 206.675, 178.201
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21N
32B
42O
53C
63P
74D
84Q
95E
105R
116F
126S
137G
147T
158H
168U
179I
189V
1910J
2010W
2111K
2211X
2312L
2412Y
2513M
2613Z

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 526
2116N1 - 526
3226B1 - 229
4226O1 - 229
5336C1 - 272
6336P1 - 272
7446D4 - 147
8446Q4 - 147
9556E5 - 109
10556R5 - 109
11666F1 - 99
12666S1 - 99
13776G1 - 85
14776T1 - 85
15886H7 - 85
16886U7 - 85
17996I1 - 73
18996V1 - 73
1910106J1 - 59
2010106W1 - 59
2111116K6 - 54
2211116X6 - 54
2312126L2 - 47
2412126Y2 - 47
2513136M1 - 43
2613136Z1 - 43

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

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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, cytochrome-c oxidase
#3: Protein Cytochrome c oxidase subunit 3 / Cytochrome c oxidase polypeptide III


Mass: 29957.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00415, cytochrome-c oxidase
#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, cytochrome-c oxidase
#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, cytochrome-c oxidase
#6: Protein Cytochrome c oxidase subunit 5B, mitochondrial / 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, cytochrome-c oxidase
#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 (cattle) / References: UniProt: P07471, cytochrome-c oxidase
#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 (cattle) / References: UniProt: P00429, cytochrome-c oxidase
#9: Protein Cytochrome c oxidase subunit 6C / Cytochrome c oxidase polypeptide VIc / Cytochrome c oxidase subunit STA


Mass: 8537.019 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P04038, cytochrome-c oxidase
#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 (cattle) / References: UniProt: P07470, cytochrome-c oxidase
#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 (cattle) / References: UniProt: P13183, cytochrome-c oxidase
#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 (cattle) / References: UniProt: P00430, cytochrome-c oxidase
#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 (cattle) / References: UniProt: P10175, cytochrome-c oxidase

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Sugars , 1 types, 4 molecules

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


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

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Non-polymers , 15 types, 1336 molecules

#14: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#15: Chemical
ChemComp-HEA / HEME-A


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


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


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#19: Chemical
ChemComp-TGL / TRISTEAROYLGLYCEROL / TRIACYLGLYCEROL


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


Mass: 749.007 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#21: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


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


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


Num. of mol.: 2 / Source method: obtained synthetically
#24: 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
#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-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
#27: 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.: 1286 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.12 Å3/Da / Density % sol: 70.17 %
Crystal growTemperature: 277 K / Method: batch / pH: 6.8
Details: 40mM Sodium phosphate, 0.2% decylmaltoside, PEG 4000, pH 6.8, batch, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 451915 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 18.5
Reflection shellResolution: 2→2.02 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.2038 / Mean I/σ(I) obs: 1.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
X-PLORmodel building
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DYR

2dyr


Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 7.576 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21437 22863 5.1 %RANDOM
Rwork0.18678 ---
obs0.18818 428820 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.026 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å20 Å20 Å2
2--1.72 Å20 Å2
3----3.03 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28506 0 2172 1286 31964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.02531777
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3322.01842838
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4353556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89122.9761230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.092154718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.77715124
X-RAY DIFFRACTIONr_chiral_restr0.1730.24522
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.02723106
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4051.517847
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.324228836
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.502313930
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1754.514002
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A4478loose positional0.135
22B1878loose positional0.255
33C2709loose positional0.185
44D1195loose positional0.295
55E852loose positional0.285
66F749loose positional0.435
77G705loose positional0.225
88H662loose positional0.245
99I601loose positional0.45
1010J461loose positional0.25
1111K385loose positional0.25
1212L380loose positional0.35
1313M336loose positional0.25
11N4478loose thermal1.6910
22O1878loose thermal3.0410
33P2709loose thermal1.8610
44Q1195loose thermal7.7210
55R852loose thermal2.6710
66S749loose thermal2.4910
77T705loose thermal1.6810
88U662loose thermal2.6510
99V601loose thermal4.1410
1010W461loose thermal2.1910
1111X385loose thermal2.6710
1212Y380loose thermal1.8910
1313Z336loose thermal3.3210
LS refinement shellResolution: 2.001→2.022 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.327 658 -
Rwork0.304 12500 -
obs--98.57 %
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)
10.25130.0084-0.08550.1808-0.01280.3573-0.0030.0240.01920.00990.015-0.0086-0.0134-0.0241-0.0120.0411-0.0256-0.01620.02460.00580.022662.3207310.4231199.0524
20.46330.15830.14240.29690.02730.46680.03060.1244-0.15130.04970.0276-0.1559-0.03670.1025-0.05820.042-0.0294-0.0220.0712-0.0450.1892126.5752315.4087195.1786
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 514
2X-RAY DIFFRACTION1A601 - 606
3X-RAY DIFFRACTION1A607 - 609
4X-RAY DIFFRACTION1B1 - 227
5X-RAY DIFFRACTION1B301
6X-RAY DIFFRACTION1C3 - 261
7X-RAY DIFFRACTION1C301 - 304
8X-RAY DIFFRACTION1G101 - 102
9X-RAY DIFFRACTION1D4 - 147
10X-RAY DIFFRACTION1E5 - 109
11X-RAY DIFFRACTION1F1 - 98
12X-RAY DIFFRACTION1F101
13X-RAY DIFFRACTION1G1 - 84
14X-RAY DIFFRACTION1H7 - 85
15X-RAY DIFFRACTION1I1 - 73
16X-RAY DIFFRACTION1J1 - 58
17X-RAY DIFFRACTION1K6 - 54
18X-RAY DIFFRACTION1L2 - 47
19X-RAY DIFFRACTION1M1 - 43
20X-RAY DIFFRACTION1A701 - 708
21X-RAY DIFFRACTION1B401 - 408
22X-RAY DIFFRACTION1D301 - 303
23X-RAY DIFFRACTION1K101 - 102
24X-RAY DIFFRACTION1A710
25X-RAY DIFFRACTION1B409 - 428
26X-RAY DIFFRACTION1H101 - 107
27X-RAY DIFFRACTION1A711 - 713
28X-RAY DIFFRACTION1D304 - 305
29X-RAY DIFFRACTION1K103
30X-RAY DIFFRACTION1A714 - 728
31X-RAY DIFFRACTION1A729 - 735
32X-RAY DIFFRACTION1A736 - 740
33X-RAY DIFFRACTION1A741 - 747
34X-RAY DIFFRACTION1A748 - 753
35X-RAY DIFFRACTION1A754 - 769
36X-RAY DIFFRACTION1B429 - 435
37X-RAY DIFFRACTION2N1 - 514
38X-RAY DIFFRACTION2N601 - 606
39X-RAY DIFFRACTION2O1 - 227
40X-RAY DIFFRACTION2O301 - 302
41X-RAY DIFFRACTION2P3 - 261
42X-RAY DIFFRACTION2P301
43X-RAY DIFFRACTION2Q4 - 147
44X-RAY DIFFRACTION2R5 - 109
45X-RAY DIFFRACTION2S1 - 98
46X-RAY DIFFRACTION2S101
47X-RAY DIFFRACTION2T1 - 84
48X-RAY DIFFRACTION2U7 - 85
49X-RAY DIFFRACTION2V1 - 73
50X-RAY DIFFRACTION2W1 - 58
51X-RAY DIFFRACTION2X6 - 54
52X-RAY DIFFRACTION2Y2 - 47
53X-RAY DIFFRACTION2Z1 - 43
54X-RAY DIFFRACTION2N702 - 708
55X-RAY DIFFRACTION2O402 - 410
56X-RAY DIFFRACTION2Q301 - 302
57X-RAY DIFFRACTION2X101 - 103
58X-RAY DIFFRACTION2O411 - 430
59X-RAY DIFFRACTION2U101 - 107
60X-RAY DIFFRACTION2N709 - 710
61X-RAY DIFFRACTION2Q303 - 305
62X-RAY DIFFRACTION2X104
63X-RAY DIFFRACTION2N711 - 724
64X-RAY DIFFRACTION2P402
65X-RAY DIFFRACTION2N725 - 732
66X-RAY DIFFRACTION2N733 - 737
67X-RAY DIFFRACTION2N738 - 743
68X-RAY DIFFRACTION2N744 - 749
69X-RAY DIFFRACTION2N750 - 764
70X-RAY DIFFRACTION2O431 - 438

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