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- PDB-1cyx: QUINOL OXIDASE (PERIPLASMIC FRAGMENT OF SUBUNIT II WITH ENGINEERE... -

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Basic information

Entry
Database: PDB / ID: 1cyx
TitleQUINOL OXIDASE (PERIPLASMIC FRAGMENT OF SUBUNIT II WITH ENGINEERED CU-A BINDING SITE)(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 / electron transport coupled proton transport / cytochrome-c oxidase activity / proton transmembrane transporter activity / ATP synthesis coupled electron transport / respirasome ...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 / electron transport coupled proton transport / cytochrome-c oxidase activity / proton transmembrane transporter activity / ATP synthesis coupled electron transport / respirasome / 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
DINUCLEAR COPPER ION / Cytochrome bo(3) ubiquinol oxidase subunit 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.3 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: J.Biol.Chem. / Year: 1993
Title: Two Cysteines, Two Histidines and One Methionine are Ligands of a Binuclear Purple Copper Center
Authors: Kelly, M. / Lappalainen, P. / Talbo, G. / Haltia, T. / Van Der Oost, J. / Saraste, M.
#3: 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: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_label_atom_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_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_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_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8702
Polymers22,7431
Non-polymers1271
Water3,027168
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.000, 98.200, 39.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYOA


Mass: 22742.748 Da / Num. of mol.: 1 / Fragment: PERIPLASMIC FRAGMENT (RESIDUES 111 - 315) / Mutation: N172H, S207C, S209E, Y210I, S211C, F215H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET.E6 / Production host: Escherichia coli (E. coli)
References: UniProt: P0ABJ1, Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor
#2: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 1.98 Å3/Da / Density % sol: 37.88 %
Crystal growpH: 4.5 / Details: pH 4.5
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-20 mg/mlprotein1drop
220 mMTris-HCl1drop
320 %(w/v)PEG60001reservoir
4180 mMacetic acid1reservoir
520 mMsodium acetate1reservoir
650 mMammonium sulfate1reservoir
71 mM1reservoirNaN3

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→1000 Å / Num. obs: 8265 / % possible obs: 87.3 % / Observed criterion σ(I): 0 / Redundancy: 3.19 % / Rmerge(I) obs: 0.096
Reflection
*PLUS
Num. obs: 7426 / Num. measured all: 17363 / Rmerge(I) obs: 0.084

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.3→6 Å / σ(F): 1
RfactorNum. reflection
Rfree0.316 -
Rwork0.196 -
obs0.196 7426
Displacement parametersBiso mean: 16.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1235 0 2 168 1405
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.584
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.27
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.39
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_deg26.27
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.39

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