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- PDB-8z5b: The X-Ray crystal structure of multicopper oxidase from Bacillus ... -

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Basic information

Entry
Database: PDB / ID: 8z5b
TitleThe X-Ray crystal structure of multicopper oxidase from Bacillus freudenreichii
ComponentsMulticopper oxidase
KeywordsOXIDOREDUCTASE / Oxidized polyphenol substrates
Function / homologyCOPPER (II) ION / :
Function and homology information
Biological speciesBacillus freudenreichii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsQian, H. / Wang, Y.
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: Multicopper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8344
Polymers63,6521
Non-polymers1823
Water11,295627
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.590, 74.590, 230.946
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Multicopper oxidase


Mass: 63651.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus freudenreichii (bacteria) / Production host: Escherichia coli (E. coli) / References: cuproxidase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / 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: 2.52 Å3/Da / Density % sol: 51.25 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 20% v/v Ethanol

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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 EIGER2 S 9M / Detector: PIXEL / Date: Oct 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.4→29.02 Å / Num. obs: 124244 / % possible obs: 96.3 % / Redundancy: 14.3 % / CC1/2: 0.998 / Net I/σ(I): 24.2
Reflection shellResolution: 1.4→1.45 Å / Num. unique obs: 124244 / Rrim(I) all: 0.03

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→29.02 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1731 2000 1.61 %
Rwork0.1584 --
obs0.1587 124244 96.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→29.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4126 0 3 627 4756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084271
X-RAY DIFFRACTIONf_angle_d1.0415822
X-RAY DIFFRACTIONf_dihedral_angle_d6.554563
X-RAY DIFFRACTIONf_chiral_restr0.093625
X-RAY DIFFRACTIONf_plane_restr0.011757
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.36821230.3167526X-RAY DIFFRACTION84
1.43-1.470.27161290.2437884X-RAY DIFFRACTION89
1.47-1.520.21681330.19868145X-RAY DIFFRACTION91
1.52-1.570.2011380.17628415X-RAY DIFFRACTION94
1.57-1.620.1951420.16558653X-RAY DIFFRACTION96
1.62-1.690.17071430.16548758X-RAY DIFFRACTION98
1.69-1.760.16611440.16898813X-RAY DIFFRACTION98
1.76-1.860.18691470.16018944X-RAY DIFFRACTION99
1.86-1.970.18881470.168982X-RAY DIFFRACTION100
1.97-2.130.16641470.15139050X-RAY DIFFRACTION100
2.13-2.340.16791490.15449081X-RAY DIFFRACTION100
2.34-2.680.1831490.15739141X-RAY DIFFRACTION100
2.68-3.370.14531520.15429248X-RAY DIFFRACTION100
3.37-29.020.16211570.14289604X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.37850.64230.21961.7746-0.54180.9274-0.07120.4233-0.0204-0.10470.0573-0.0485-0.00270.07290.01460.12860.00180.03030.1488-0.00870.05976.010937.610275.091
21.16120.1644-0.06881.1458-0.27560.6982-0.03760.1087-0.0987-0.03130.0620.13780.0106-0.0793-0.02280.0839-0.0097-0.00040.12560.00550.10965.015927.928182.6293
31.0654-0.54480.12281.9049-0.70670.6772-0.05970.04720.04790.14050.0371-0.0719-0.12180.01120.02370.1171-0.0095-0.01380.11880.01420.088876.078341.582286.286
41.5817-0.2739-0.191.44-0.43831.0584-0.06670.07760.21450.23430.09860.0681-0.2024-0.121-0.05540.19630.0231-0.0140.11130.01490.117668.251850.382389.3502
51.4053-0.4448-0.29421.3315-0.10180.6977-0.1297-0.1778-0.13830.5310.19830.1427-0.1248-0.0969-0.03650.30160.07370.04280.2360.07330.14665.484729.545106.4608
60.07960.05140.06140.3247-0.4173.0697-0.0461-0.05410.02770.42160.11110.0029-0.37710.2115-0.06730.38250.08560.01750.20740.01420.148964.987544.0756108.9792
71.2894-0.3306-0.0031.3974-0.32221.3785-0.0761-0.0644-0.10730.27010.16060.2513-0.1581-0.1829-0.07280.20820.05990.05460.17940.06490.140261.68232.4286100.7821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 44 through 76 )
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 233 )
3X-RAY DIFFRACTION3chain 'A' and (resid 234 through 331 )
4X-RAY DIFFRACTION4chain 'A' and (resid 332 through 418 )
5X-RAY DIFFRACTION5chain 'A' and (resid 419 through 463 )
6X-RAY DIFFRACTION6chain 'A' and (resid 464 through 505 )
7X-RAY DIFFRACTION7chain 'A' and (resid 506 through 550 )

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