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- PDB-2y69: Bovine heart cytochrome c oxidase re-refined with molecular oxygen -

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Basic information

Entry
Database: PDB / ID: 2y69
TitleBovine heart cytochrome c oxidase re-refined with molecular oxygen
Components
  • (CYTOCHROME C OXIDASE POLYPEPTIDE ...) x 5
  • (CYTOCHROME C OXIDASE SUBUNIT ...) x 8
KeywordsELECTRON TRANSPORT / COMPLEX IV / PROTON PUMPS / MEMBRANE PROTEIN
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
CHOLIC ACID / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / OXYGEN MOLECULE / Chem-PEK / Chem-PGV / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 4 isoform 1, mitochondrial ...CHOLIC ACID / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / OXYGEN MOLECULE / Chem-PEK / Chem-PGV / 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 / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKaila, V.R.I. / Oksanen, E. / Goldman, A. / Verkhovsky, M.I. / Sundholm, D. / Wikstrom, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: A Peroxide Bridge between Fe and Cu Ions in the O2 Reduction Site of Fully Oxidized Cytochrome C Oxidase Could Suppress the Proton Pump.
Authors: Aoyama, H. / Muramoto, K. / Shinzawa-Itoh, K. / Hirata, K. / Yamashita, E. / Tsukihara, T. / Ogura, T. / Yoshikawa, S.
History
DepositionJan 20, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references / Other / Version format compliance
Revision 1.2Feb 4, 2015Group: Atomic model / Derived calculations / Other
Revision 1.3Jun 20, 2018Group: Advisory / Data collection / Category: pdbx_unobs_or_zero_occ_atoms
Revision 1.4Jul 31, 2019Group: Advisory / Data collection / Derived calculations
Category: database_PDB_caveat / pdbx_struct_conn_angle ...database_PDB_caveat / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Revision 1.5Nov 6, 2019Group: Data collection / Database references / Other / Category: pdbx_database_related / pdbx_database_status / Item: _pdbx_database_status.status_code_sf
Revision 1.6Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_conn_type / struct_site
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.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 / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 0THIS ENTRY 2Y69 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R3ABMSF) ...THIS ENTRY 2Y69 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R3ABMSF) DETERMINED BY AUTHORS OF THE PDB ENTRY 3ABM: H.AOYAMA,K.MURAMOTO,K.SHINZAWA-ITOH,K.HIRATA,E.YAMASHITA, T.TSUKIHARA,T.OGURA,S.YOSHIKAWA

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME C OXIDASE SUBUNIT 1
B: CYTOCHROME C OXIDASE SUBUNIT 2
C: CYTOCHROME C OXIDASE SUBUNIT 3
D: CYTOCHROME C OXIDASE SUBUNIT 4 ISOFORM 1
E: CYTOCHROME C OXIDASE SUBUNIT 5A
F: CYTOCHROME C OXIDASE SUBUNIT 5B
G: CYTOCHROME C OXIDASE POLYPEPTIDE 6A2
H: CYTOCHROME C OXIDASE SUBUNIT VIB ISOFORM 1
I: CYTOCHROME C OXIDASE POLYPEPTIDE VIC
J: CYTOCHROME C OXIDASE POLYPEPTIDE 7A1
K: CYTOCHROME C OXIDASE POLYPEPTIDE 7B
L: CYTOCHROME C OXIDASE SUBUNIT 7C
M: CYTOCHROME C OXIDASE POLYPEPTIDE 8H
N: CYTOCHROME C OXIDASE SUBUNIT 1
O: CYTOCHROME C OXIDASE SUBUNIT 2
P: CYTOCHROME C OXIDASE SUBUNIT 3
Q: CYTOCHROME C OXIDASE SUBUNIT 4 ISOFORM 1
R: CYTOCHROME C OXIDASE SUBUNIT 5A
S: CYTOCHROME C OXIDASE SUBUNIT 5B
T: CYTOCHROME C OXIDASE POLYPEPTIDE 6A2
U: CYTOCHROME C OXIDASE SUBUNIT VIB ISOFORM 1
V: CYTOCHROME C OXIDASE POLYPEPTIDE VIC
W: CYTOCHROME C OXIDASE POLYPEPTIDE 7A1
X: CYTOCHROME C OXIDASE POLYPEPTIDE 7B
Y: CYTOCHROME C OXIDASE SUBUNIT 7C
Z: CYTOCHROME C OXIDASE POLYPEPTIDE 8H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)464,22554
Polymers452,24026
Non-polymers11,98528
Water18,8801048
1
A: CYTOCHROME C OXIDASE SUBUNIT 1
B: CYTOCHROME C OXIDASE SUBUNIT 2
C: CYTOCHROME C OXIDASE SUBUNIT 3
D: CYTOCHROME C OXIDASE SUBUNIT 4 ISOFORM 1
E: CYTOCHROME C OXIDASE SUBUNIT 5A
F: CYTOCHROME C OXIDASE SUBUNIT 5B
H: CYTOCHROME C OXIDASE SUBUNIT VIB ISOFORM 1
I: CYTOCHROME C OXIDASE POLYPEPTIDE VIC
J: CYTOCHROME C OXIDASE POLYPEPTIDE 7A1
K: CYTOCHROME C OXIDASE POLYPEPTIDE 7B
L: CYTOCHROME C OXIDASE SUBUNIT 7C
M: CYTOCHROME C OXIDASE POLYPEPTIDE 8H
T: CYTOCHROME C OXIDASE POLYPEPTIDE 6A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,11227
Polymers226,12013
Non-polymers5,99214
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60720 Å2
ΔGint-501 kcal/mol
Surface area64280 Å2
MethodPISA
2
G: CYTOCHROME C OXIDASE POLYPEPTIDE 6A2
N: CYTOCHROME C OXIDASE SUBUNIT 1
O: CYTOCHROME C OXIDASE SUBUNIT 2
P: CYTOCHROME C OXIDASE SUBUNIT 3
Q: CYTOCHROME C OXIDASE SUBUNIT 4 ISOFORM 1
R: CYTOCHROME C OXIDASE SUBUNIT 5A
S: CYTOCHROME C OXIDASE SUBUNIT 5B
U: CYTOCHROME C OXIDASE SUBUNIT VIB ISOFORM 1
V: CYTOCHROME C OXIDASE POLYPEPTIDE VIC
W: CYTOCHROME C OXIDASE POLYPEPTIDE 7A1
X: CYTOCHROME C OXIDASE POLYPEPTIDE 7B
Y: CYTOCHROME C OXIDASE SUBUNIT 7C
Z: CYTOCHROME C OXIDASE POLYPEPTIDE 8H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,11227
Polymers226,12013
Non-polymers5,99214
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60630 Å2
ΔGint-503.9 kcal/mol
Surface area64650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.697, 206.991, 178.251
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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CYTOCHROME C OXIDASE SUBUNIT ... , 8 types, 16 molecules ANBOCPDQERFSHULY

#1: Protein CYTOCHROME C OXIDASE SUBUNIT 1 / CYTOCHROME C OXIDASE POLYPEPTIDE I


Mass: 57065.844 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: 26040.393 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic 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 (domestic cattle) / References: UniProt: P00415, cytochrome-c oxidase
#4: Protein CYTOCHROME C OXIDASE SUBUNIT 4 ISOFORM 1 / CYTOCHROME C OXIDASE SUBUNIT IV ISOFORM 1 / COX IV- 1 / CYTOCHROME C OXIDASE POLYPEPTIDE IV


Mass: 19602.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / References: UniProt: P00423, cytochrome-c oxidase
#5: Protein CYTOCHROME C OXIDASE SUBUNIT 5A / CYTOCHROME C OXIDASE POLYPEPTIDE VA


Mass: 16758.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / References: UniProt: P00426, cytochrome-c oxidase
#6: Protein CYTOCHROME C OXIDASE SUBUNIT 5B / CYTOCHROME C OXIDASE POLYPEPTIDE VB / CYTOCHROME C OXIDASE POLYPEPTIDE VIA


Mass: 13852.807 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / References: UniProt: P00428, cytochrome-c oxidase
#8: Protein CYTOCHROME C OXIDASE SUBUNIT VIB ISOFORM 1 / COX VIB-1 / CYTOCHROME C OXIDASE POLYPEPTIDE VII / CYTOCHROME C OXIDASE SUBUNIT AED


Mass: 10170.439 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / References: UniProt: P00429, cytochrome-c oxidase
#12: Protein CYTOCHROME C OXIDASE SUBUNIT 7C / CYTOCHROME C OXIDASE POLYPEPTIDE VIIC / CYTOCHROME C OXIDASE POLYPEPTIDE VIIIA


Mass: 7342.661 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / References: UniProt: P00430, cytochrome-c oxidase

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CYTOCHROME C OXIDASE POLYPEPTIDE ... , 5 types, 10 molecules GTIVJWKXMZ

#7: Protein CYTOCHROME C OXIDASE POLYPEPTIDE 6A2 / CYTOCHROME C OXIDASE POLYPEPTIDE VIA-HEART / COXVIAH / POLYPEPTIDE VIB


Mass: 10899.382 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / References: UniProt: P07471, cytochrome-c oxidase
#9: Protein CYTOCHROME C OXIDASE POLYPEPTIDE VIC / STA


Mass: 8626.179 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / References: UniProt: P04038, cytochrome-c oxidase
#10: Protein CYTOCHROME C OXIDASE POLYPEPTIDE 7A1 / CYTOCHROME C OXIDASE POLYPEPTIDE VIIA-HEART / CYTOCHROME C OXIDASE SUBUNIT VIIA-H / COX VIIA-M / VIIIC


Mass: 9076.522 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / References: UniProt: P07470, cytochrome-c oxidase
#11: Protein CYTOCHROME C OXIDASE POLYPEPTIDE 7B / CYTOCHROME C OXIDASE POLYPEPTIDE VIIB / IHQ


Mass: 9077.439 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / References: UniProt: P13183, cytochrome-c oxidase
#13: Protein CYTOCHROME C OXIDASE POLYPEPTIDE 8H / CYTOCHROME C OXIDASE POLYPEPTIDE VIII-HEART / CYTOCHROME C OXIDASE SUBUNIT 8-1 / VIIIB / IX


Mass: 7650.059 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / References: UniProt: P10175, cytochrome-c oxidase

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Sugars , 1 types, 2 molecules

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


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 10 types, 1074 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-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#17: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#18: Chemical
ChemComp-CHD / CHOLIC ACID


Mass: 408.571 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H40O5
#19: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2
#20: 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.: 2 / Source method: obtained synthetically / Formula: C43H78NO8P / Comment: phospholipid*YM
#21: 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.: 4 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#22: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 1048 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.75 Å3/Da / Density % sol: 67.17 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 3ABM

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionBiso Wilson estimate: 0 Å2

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Processing

SoftwareName: REFMAC / Version: 5.5.0066 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→64.15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.281 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA R3ABMSF.
RfactorNum. reflection% reflectionSelection details
Rfree0.24546 16433 3.5 %RANDOM
Rwork0.21062 ---
obs0.21207 455500 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.538 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20 Å20 Å2
2--1.37 Å20 Å2
3----2.4 Å2
Refinement stepCycle: LAST / Resolution: 1.95→64.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28264 0 804 1048 30116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02230046
X-RAY DIFFRACTIONr_bond_other_d0.0130.02230046
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.97140854
X-RAY DIFFRACTIONr_angle_other_deg1.4691.97140854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.40753502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14922.9741224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.098154646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.49115124
X-RAY DIFFRACTIONr_chiral_restr0.0910.24416
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02122432
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02122432
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_it0.7481.53686
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.24525988
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.23132489
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9994.52440
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
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 1503 -
Rwork0.318 30851 -
obs--100 %

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