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- PDB-1cyw: QUINOL OXIDASE (PERIPLASMIC FRAGMENT OF SUBUNIT II) (CYOA) -

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Basic information

Entry
Database: PDB / ID: 1cyw
TitleQUINOL OXIDASE (PERIPLASMIC FRAGMENT OF SUBUNIT II) (CYOA)
ComponentsCYOA
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


cytochrome o ubiquinol oxidase complex / oxidoreduction-driven active transmembrane transporter activity / cytochrome bo3 ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / cytochrome-c oxidase activity / proton transmembrane transporter activity / : / electron transport coupled proton transport / ATP synthesis coupled electron transport ...cytochrome o ubiquinol oxidase complex / oxidoreduction-driven active transmembrane transporter activity / cytochrome bo3 ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / cytochrome-c oxidase activity / proton transmembrane transporter activity / : / electron transport coupled proton transport / ATP synthesis coupled electron transport / aerobic respiration / electron transfer activity / copper ion binding / plasma membrane
Similarity search - Function
COX aromatic rich motif / COX Aromatic Rich Motif / Cytochrome o ubiquinol oxidase subunit II / Ubiquinol oxidase subunit 2, cupredoxin domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c/quinol oxidase subunit II / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal ...COX aromatic rich motif / COX Aromatic Rich Motif / Cytochrome o ubiquinol oxidase subunit II / Ubiquinol oxidase subunit 2, cupredoxin domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c/quinol oxidase subunit II / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cupredoxins - blue copper proteins / Cupredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cytochrome bo(3) ubiquinol oxidase subunit 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsWilmanns, M. / Lappalainen, P. / Kelly, M. / Sauer-Eriksson, E. / Saraste, M.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Crystal structure of the membrane-exposed domain from a respiratory quinol oxidase complex with an engineered dinuclear copper center.
Authors: Wilmanns, M. / Lappalainen, P. / Kelly, M. / Sauer-Eriksson, E. / Saraste, M.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary X-Ray Analysis of the Periplasmic Fragment of Cyoa-A Subunit of the Escherichia Coli Cytochrome O Complex
Authors: Van Der Oost, J. / Musacchio, A. / Pauptit, R.A. / Ceska, T.A. / Wierenga, R.K. / Saraste, M.
#2: Journal: Embo J. / Year: 1992
Title: Restoration of a Lost Metal-Binding Site: Construction of Two Different Copper Sites Into a Subunit of the E. Coli Cytochrome O Quinol Oxidase Complex
Authors: Van Der Oost, J. / Lappalainen, P. / Musacchio, A. / Warne, A. / Lemieux, L. / Rumbley, J. / Gennis, R.B. / Aasa, R. / Pascher, T. / Malmstrom, B.M. / Saraste, M.
History
DepositionAug 22, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Aug 17, 2022Group: Data collection / Database references / Experimental preparation
Category: database_2 / diffrn_detector ...database_2 / diffrn_detector / diffrn_radiation / exptl_crystal
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_detector.pdbx_collection_date / _diffrn_radiation.pdbx_diffrn_protocol / _exptl_crystal.description
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYOA


Theoretical massNumber of molelcules
Total (without water)22,7041
Polymers22,7041
Non-polymers00
Water82946
1
A: CYOA

A: CYOA


Theoretical massNumber of molelcules
Total (without water)45,4072
Polymers45,4072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area1230 Å2
ΔGint-10 kcal/mol
Surface area13690 Å2
MethodPISA, PQS
2
A: CYOA

A: CYOA

A: CYOA

A: CYOA


Theoretical massNumber of molelcules
Total (without water)90,8144
Polymers90,8144
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area5200 Å2
ΔGint-43 kcal/mol
Surface area24640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.600, 84.100, 94.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein CYOA


Mass: 22703.582 Da / Num. of mol.: 1 / Fragment: PERIPLASMIC FRAGMENT (RESIDUES 111 - 315)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET.E2 / Species (production host): Escherichia coli / Gene (production host): CYOA / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P0ABJ1, Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.03 %
Description: Authors state that several data sets were collected from 1992 to 1994

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→1000 Å / Num. obs: 5943 / % possible obs: 86.3 % / Observed criterion σ(I): 0
Reflection
*PLUS
Num. measured all: 12996 / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.5→6 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.326 --
Rwork0.192 --
obs0.192 5180 81.6 %
Displacement parametersBiso mean: 32.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1239 0 0 46 1285
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.964
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.09
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.68
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.09
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.68

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