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- PDB-6nmp: SFX structure of oxidized cytochrome c oxidase at room temperature -

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Basic information

Entry
Database: PDB / ID: 6nmp
TitleSFX structure of oxidized cytochrome c oxidase at room temperature
Components(Cytochrome c oxidase subunit ...) x 13
KeywordsOXIDOREDUCTASE / complex IV / membrane protein / Terminal enzyme / electron transfer
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, 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 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, 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 / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsRousseau, D.L. / Yeh, S.-R. / Ishigami, I.
Funding support United States, 8items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM098799 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM126297 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115773 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM095583 United States
National Science Foundation (NSF, United States)STC 1231306 United States
National Science Foundation (NSF, United States)CHE-1404929 United States
National Science Foundation (NSF, United States)Bio ABI 1565180 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Snapshot of an oxygen intermediate in the catalytic reaction of cytochromecoxidase.
Authors: Ishigami, I. / Lewis-Ballester, A. / Echelmeier, A. / Brehm, G. / Zatsepin, N.A. / Grant, T.D. / Coe, J.D. / Lisova, S. / Nelson, G. / Zhang, S. / Dobson, Z.F. / Boutet, S. / Sierra, R.G. / ...Authors: Ishigami, I. / Lewis-Ballester, A. / Echelmeier, A. / Brehm, G. / Zatsepin, N.A. / Grant, T.D. / Coe, J.D. / Lisova, S. / Nelson, G. / Zhang, S. / Dobson, Z.F. / Boutet, S. / Sierra, R.G. / Batyuk, A. / Fromme, P. / Fromme, R. / Spence, J.C.H. / Ros, A. / Yeh, S.R. / Rousseau, D.L.
History
DepositionJan 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 2.0Mar 20, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / entity_poly_seq / entity_src_nat / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / struct_conf / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_nat.pdbx_end_seq_num / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_site_gen.label_seq_id
Revision 2.1Nov 27, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn
Item: _pdbx_audit_support.funding_organization / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 11, 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 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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)442,82080
Polymers410,21626
Non-polymers32,60454
Water8,575476
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)178.700, 189.800, 211.300
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 ... , 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 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: 10684.038 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, 4 molecules

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


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 14 types, 526 molecules

#14: Chemical ChemComp-CU / COPPER (II) ION


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


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#17: Chemical
ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#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-TGL / TRISTEAROYLGLYCEROL / TRIACYLGLYCEROL


Mass: 891.480 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C57H110O6
#20: Chemical ChemComp-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#21: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2
#22: 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
#23: 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: isolated from a genetically manipulated source
Formula: C81H156O17P2 / Comment: phospholipid*YM
#27: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 476 / 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: 4.36 Å3/Da / Density % sol: 71.82 %
Crystal growTemperature: 277 K / Method: batch mode / pH: 6.8
Details: 36 hour crystallization in a cold room with stirring

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.306 Å
DetectorType: CS-PAD XPP / Detector: PIXEL / Date: Dec 7, 2016 / Frequency: 120
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.306 Å / Relative weight: 1
ReflectionResolution: 2.9→15 Å / Num. obs: 150666 / % possible obs: 99.64 % / Redundancy: 204 % / CC1/2: 0.928 / Net I/σ(I): 2.8
Reflection shellResolution: 2.9→2.972 Å / Mean I/σ(I) obs: 0.43 / Num. unique obs: 10677 / CC1/2: 0.149
Serial crystallography measurementCollimation: compound refractive lense / Pulse duration: 40 fsec. / Pulse photon energy: 9.5 keV / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionDescription: GCVN / Injector temperature: 293 K

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DYR

2dyr


Resolution: 2.9→15 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.914 / SU B: 22.095 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R: 0.632 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24357 7805 4.9 %RANDOM
Rwork0.1917 ---
obs0.19428 149982 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.835 Å2
Baniso -1Baniso -2Baniso -3
1--2.46 Å20 Å2-0 Å2
2--0.72 Å20 Å2
3---1.74 Å2
Refinement stepCycle: 1 / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28506 0 2228 476 31210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0231718
X-RAY DIFFRACTIONr_bond_other_d0.0050.0230162
X-RAY DIFFRACTIONr_angle_refined_deg1.6662.00942766
X-RAY DIFFRACTIONr_angle_other_deg1.1153.00370140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.54453532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81322.9761230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.699154686
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.39615124
X-RAY DIFFRACTIONr_chiral_restr0.1040.24528
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02133004
X-RAY DIFFRACTIONr_gen_planes_other0.0040.026672
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_it3.5686.02414206
X-RAY DIFFRACTIONr_mcbond_other3.5686.02314205
X-RAY DIFFRACTIONr_mcangle_it5.8879.01617712
X-RAY DIFFRACTIONr_mcangle_other5.8879.01617713
X-RAY DIFFRACTIONr_scbond_it3.9336.73617512
X-RAY DIFFRACTIONr_scbond_other3.9336.73717511
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5379.86925055
X-RAY DIFFRACTIONr_long_range_B_refined10.21770.86834950
X-RAY DIFFRACTIONr_long_range_B_other10.21270.86734939
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.972 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 563 -
Rwork0.365 10677 -
obs--100 %

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