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- PDB-1m56: Structure of cytochrome c oxidase from Rhodobactor sphaeroides (W... -

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Basic information

Entry
Database: PDB / ID: 1m56
TitleStructure of cytochrome c oxidase from Rhodobactor sphaeroides (Wild Type)
Components(CYTOCHROME C ...) x 4
KeywordsOXIDOREDUCTASE / Membrane Protein
Function / homology
Function and homology information


aerobic electron transport chain / respiratory chain complex IV / cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / respiratory electron transport chain / copper ion binding / heme binding ...aerobic electron transport chain / respiratory chain complex IV / cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / respiratory electron transport chain / copper ion binding / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Bacterial aa3 type cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit IV, bacterial aa3 type / Bacterial aa3 type cytochrome c oxidase subunit IV superfamily / Bacterial aa3 type cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit I bacterial type / Cytochrome c oxidase, subunit III, four-helix bundle / Helix Hairpins - #90 / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase subunit III domain ...Bacterial aa3 type cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit IV, bacterial aa3 type / Bacterial aa3 type cytochrome c oxidase subunit IV superfamily / Bacterial aa3 type cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit I bacterial type / Cytochrome c oxidase, subunit III, four-helix bundle / Helix Hairpins - #90 / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase, subunit II / 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 / Cupredoxins - blue copper proteins / Cupredoxin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Four Helix Bundle (Hemerythrin (Met), subunit A) / Helix Hairpins / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / COPPER (II) ION / HEME-A / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 2 / Aa3-type cytochrome c oxidase subunit IV
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSvensson-Ek, M. / Abramson, J. / Larsson, G. / Tornroth, S. / Brezezinski, P. / Iwata, S.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: The X-ray crystal structures of wild-type and EQ(I-286) mutant cytochrome c oxidases from Rhodobacter sphaeroides.
Authors: Svensson-Ek, M. / Abramson, J. / Larsson, G. / Tornroth, S. / Brzezinski, P. / Iwata, S.
History
DepositionJul 8, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jun 30, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site / 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_comp_id / _atom_site.label_comp_id / _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.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _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_conn.pdbx_dist_value / _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_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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
B: CYTOCHROME C OXIDASE
C: CYTOCHROME C OXIDASE
D: CYTOCHROME C OXIDASE
G: CYTOCHROME C OXIDASE
H: CYTOCHROME C OXIDASE
I: CYTOCHROME C OXIDASE
J: CYTOCHROME C OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,27334
Polymers256,3758
Non-polymers12,89826
Water7,855436
1
A: CYTOCHROME C OXIDASE
B: CYTOCHROME C OXIDASE
C: CYTOCHROME C OXIDASE
D: CYTOCHROME C OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,63617
Polymers128,1874
Non-polymers6,44913
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30030 Å2
ΔGint-342 kcal/mol
Surface area37240 Å2
MethodPISA
2
G: CYTOCHROME C OXIDASE
H: CYTOCHROME C OXIDASE
I: CYTOCHROME C OXIDASE
J: CYTOCHROME C OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,63617
Polymers128,1874
Non-polymers6,44913
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30070 Å2
ΔGint-345 kcal/mol
Surface area37250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)340.360, 340.360, 89.668
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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CYTOCHROME C ... , 4 types, 8 molecules AGBHCIDJ

#1: Protein CYTOCHROME C OXIDASE / Cytochrome c oxidase polypeptide I


Mass: 63195.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / References: UniProt: P33517, cytochrome-c oxidase
#2: Protein CYTOCHROME C OXIDASE / Cytochrome c oxidase polypeptide II


Mass: 29385.436 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / References: UniProt: Q03736, cytochrome-c oxidase
#3: Protein CYTOCHROME C OXIDASE / cytochrome-c oxidase chain III


Mass: 30197.199 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / References: UniProt: P84153, cytochrome-c oxidase
#4: Protein CYTOCHROME C OXIDASE


Mass: 5409.267 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / References: UniProt: Q8KRK5, cytochrome-c oxidase

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Non-polymers , 6 types, 462 molecules

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


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Chemical
ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#9: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 3.9 Å3/Da / Density % sol: 68.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG400, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMTris-HCl1droppH8.0
20.24 %decyl maltoside1drop
310-20 mg/mlprotein1drop
418-22 %PEG4001reservoir
550-150 mM1reservoirNaCl
6100 mMsodium citrate1reservoirpH6.0
710 mMTris1reservoir
80.24 %decylmaltoside1reservoir
92.5-3 %heptanetriol1reservoir
1020 mM1reservoirMgCl2
110.014 %dodecylmaltoside1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 12, 1998
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 119260 / Num. obs: 232383 / % possible obs: 69.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.3→2.4 Å / % possible all: 36
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 119260 / Num. measured all: 232383 / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 36 % / Num. unique obs: 7880 / Num. measured obs: 20048 / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.275 1193 Random
Rwork0.236 --
all0.236 119260 -
obs0.236 119260 -
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17636 0 862 436 18934
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d0.04
Refinement
*PLUS
Lowest resolution: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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