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- PDB-8z59: The X-Ray crystal structure of multicopper oxidase from Sulfurimo... -

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Basic information

Entry
Database: PDB / ID: 8z59
TitleThe X-Ray crystal structure of multicopper oxidase from Sulfurimonas sp.
ComponentsBilirubin oxidase
KeywordsOXIDOREDUCTASE / oxidation / polyphenol
Function / homology
Function and homology information


oxidoreductase activity / copper ion binding
Similarity search - Function
Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
COPPER (II) ION / Bilirubin oxidase
Similarity search - Component
Biological speciesSulfurimonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsWang, Y. / Qian, H.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat Commun / Year: 2025
Title: ESM-Ezy: a deep learning strategy for the mining of novel multicopper oxidases with superior properties.
Authors: Qian, H. / Wang, Y. / Zhou, X. / Gu, T. / Wang, H. / Lyu, H. / Li, Z. / Li, X. / Zhou, H. / Guo, C. / Yuan, F. / Wang, Y.
History
DepositionApr 18, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 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

Downloads & links

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Assembly

Deposited unit
A: Bilirubin oxidase
B: Bilirubin oxidase
C: Bilirubin oxidase
D: Bilirubin oxidase
E: Bilirubin oxidase
F: Bilirubin oxidase
G: Bilirubin oxidase
H: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)468,11740
Polymers466,0838
Non-polymers2,03332
Water7,999444
1
A: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5155
Polymers58,2601
Non-polymers2544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5155
Polymers58,2601
Non-polymers2544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5155
Polymers58,2601
Non-polymers2544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5155
Polymers58,2601
Non-polymers2544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5155
Polymers58,2601
Non-polymers2544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5155
Polymers58,2601
Non-polymers2544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5155
Polymers58,2601
Non-polymers2544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5155
Polymers58,2601
Non-polymers2544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.636, 103.389, 131.906
Angle α, β, γ (deg.)104.86, 103.96, 98.35
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Bilirubin oxidase / Multicopper oxidase


Mass: 58260.406 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfurimonas sp. (bacteria) / Gene: C0627_00805 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2K2VPI4
#2: Chemical...
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / 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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 290.15 K / Method: liquid diffusion
Details: 1% w/v Tryptone, 0.001 M Sodium azide, 0.05 M HEPES sodium pH 7.0, 12% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.58→50 Å / Num. obs: 126901 / % possible obs: 96.5 % / Redundancy: 3.4 % / CC1/2: 0.984 / Net I/σ(I): 7.4
Reflection shellResolution: 2.58→2.62 Å / Num. unique obs: 126901 / Rrim(I) all: 14.9

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FQG

2fqg


Resolution: 2.58→39.52 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2398 1994 1.57 %
Rwork0.1913 --
obs0.1921 126669 95.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.58→39.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28659 0 0 444 29103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0129318
X-RAY DIFFRACTIONf_angle_d1.34839614
X-RAY DIFFRACTIONf_dihedral_angle_d13.1253782
X-RAY DIFFRACTIONf_chiral_restr0.0694390
X-RAY DIFFRACTIONf_plane_restr0.0085058
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.640.3391160.28257214X-RAY DIFFRACTION77
2.64-2.710.32211290.28758136X-RAY DIFFRACTION88
2.71-2.790.32411390.27468793X-RAY DIFFRACTION94
2.79-2.880.30011440.26488985X-RAY DIFFRACTION97
2.88-2.990.32621460.2599114X-RAY DIFFRACTION98
2.99-3.110.34291470.24799100X-RAY DIFFRACTION98
3.11-3.250.28691460.22899150X-RAY DIFFRACTION99
3.25-3.420.28521450.21459116X-RAY DIFFRACTION99
3.42-3.630.27081480.19789183X-RAY DIFFRACTION99
3.63-3.910.2261480.17659192X-RAY DIFFRACTION99
3.91-4.310.19031470.15679194X-RAY DIFFRACTION99
4.31-4.930.17221450.13729177X-RAY DIFFRACTION99
4.93-6.210.21031490.15329220X-RAY DIFFRACTION99
6.21-39.520.1931450.16039101X-RAY DIFFRACTION98

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