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- PDB-8r4h: Crystal structure of the copper efflux oxidase (CueO) from Hafnia... -

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Basic information

Entry
Database: PDB / ID: 8r4h
TitleCrystal structure of the copper efflux oxidase (CueO) from Hafnia alvei deleted of the Met-rich domain
ComponentsCopper efflux oxidase,Multicopper 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 / Multicopper oxidase CueO
Similarity search - Component
Biological speciesHafnia alvei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.937 Å
AuthorsLeone, P. / Contaldo, U.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: To Be Published
Title: Crystal structure of the copper efflux oxidase (CueO) from Hafnia alvei deleted of the Met-rich domain
Authors: Leone, P. / Contaldo, U.
History
DepositionNov 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Copper efflux oxidase,Multicopper oxidase
B: Copper efflux oxidase,Multicopper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,94222
Polymers99,6892
Non-polymers1,25320
Water2,576143
1
A: Copper efflux oxidase,Multicopper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,40910
Polymers49,8441
Non-polymers5659
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Copper efflux oxidase,Multicopper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,53312
Polymers49,8441
Non-polymers68911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.273, 169.273, 90.387
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Copper efflux oxidase,Multicopper oxidase


Mass: 49844.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hafnia alvei (bacteria) / Gene: cueO, AT03_17850 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A377PPH3, UniProt: A0A097R5T5
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 8 / 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.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 100 mM CHES/ Sodium hydroxide pH 9.5 200 mM Sodium chloride 1260 mM Ammonium sulfate

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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: 2.937→48.46 Å / Num. obs: 20565 / % possible obs: 99.7 % / Redundancy: 10.7 % / CC1/2: 0.996 / Net I/σ(I): 10.4
Reflection shellResolution: 2.94→3.1 Å / Num. unique obs: 3008 / CC1/2: 0.642

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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: 2.937→30.23 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.899 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.404
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 1014 4.93 %RANDOM
Rwork0.1979 ---
obs0.2002 20551 99.7 %-
Displacement parametersBiso mean: 72.82 Å2
Baniso -1Baniso -2Baniso -3
1--6.9159 Å20 Å20 Å2
2---6.9159 Å20 Å2
3---13.8318 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.937→30.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6824 0 56 143 7023
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0077042HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.939552HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2390SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1168HARMONIC5
X-RAY DIFFRACTIONt_it7042HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.69
X-RAY DIFFRACTIONt_other_torsion17.79
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion904SEMIHARMONIC5
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_contact5749SEMIHARMONIC4
LS refinement shellResolution: 2.94→2.96 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.4451 -5.34 %
Rwork0.3033 390 -
all0.3099 412 -
obs--87.79 %

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