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- PDB-8r4f: Crystal structure of the native copper efflux oxidase (CueO) from... -

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Basic information

Entry
Database: PDB / ID: 8r4f
TitleCrystal structure of the native copper efflux oxidase (CueO) from Hafnia alvei
ComponentsCopper efflux oxidase
KeywordsMETAL BINDING PROTEIN / bacterial copper hemostasis / multi copper oxidase
Function / homology
Function and homology information


cuproxidase / oxidoreductase activity / copper ion binding
Similarity search - Function
Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / Multicopper oxidase CueO
Similarity search - Component
Biological speciesHafnia alvei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.186 Å
AuthorsLeone, P. / Contaldo, U.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Jacs Au / Year: 2025
Title: How the Larger Methionine-Rich Domain of CueO from Hafnia alvei Enhances Cuprous Oxidation.
Authors: Contaldo, U. / Santucci, P. / Vergnes, A. / Leone, P. / Becam, J. / Biaso, F. / Ilbert, M. / Ezraty, B. / Lojou, E. / Mazurenko, I.
History
DepositionNov 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Copper efflux oxidase
B: Copper efflux oxidase
C: Copper efflux oxidase
D: Copper efflux oxidase
E: Copper efflux oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,67521
Polymers288,6685
Non-polymers1,00816
Water5,314295
1
A: Copper efflux oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9234
Polymers57,7341
Non-polymers1893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Copper efflux oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9855
Polymers57,7341
Non-polymers2514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Copper efflux oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9234
Polymers57,7341
Non-polymers1893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Copper efflux oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9234
Polymers57,7341
Non-polymers1893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Copper efflux oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9234
Polymers57,7341
Non-polymers1893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.530, 167.277, 229.621
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
Copper efflux oxidase


Mass: 57733.520 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hafnia alvei (bacteria) / Gene: cueO / Production host: Escherichia coli (E. coli) / References: UniProt: A0A377PPH3
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.01 Å3/Da / Density % sol: 59.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100 mM Sodium citrate/ Citric acid pH 5.5, 20% (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 3.18→47 Å / Num. obs: 59157 / % possible obs: 99.9 % / Redundancy: 7.6 % / CC1/2: 0.993 / Net I/σ(I): 8.8
Reflection shellResolution: 3.18→3.36 Å / Num. unique obs: 8526 / CC1/2: 0.715

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (26-JUL-2023)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.186→46.56 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.895 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.432
RfactorNum. reflection% reflectionSelection details
Rfree0.2463 2993 5.07 %RANDOM
Rwork0.2165 ---
obs0.218 59083 99.9 %-
Displacement parametersBiso mean: 80.53 Å2
Baniso -1Baniso -2Baniso -3
1--15.8489 Å20 Å20 Å2
2--11.773 Å20 Å2
3---4.0759 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 3.186→46.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18269 0 34 295 18598
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00718762HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.925447HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6418SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3123HARMONIC5
X-RAY DIFFRACTIONt_it18762HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion17.01
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2403SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14983SEMIHARMONIC4
LS refinement shellResolution: 3.19→3.21 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.44 -5.75 %
Rwork0.3293 1114 -
all0.3355 1182 -
obs--96.53 %

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