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- PDB-3p0k: Structure of Baculovirus Sulfhydryl Oxidase Ac92 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3p0k
TitleStructure of Baculovirus Sulfhydryl Oxidase Ac92
Componentssulfhydryl oxidase
KeywordsOxidoreductase / Viral protein / 4-helix bundle / 5-helix bundle / flavin adenine dinucleotide / sulfhydryl oxidase
Function / homology
Function and homology information


thiol oxidase / thiol oxidase activity / host cell cytoplasm / host cell nucleus
Similarity search - Function
FAD-linked sulfhydryl oxidase / Baculovirus P33
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / IMIDAZOLE / FAD-linked sulfhydryl oxidase
Similarity search - Component
Biological speciesAutographa californica nucleopolyhedrovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.47 Å
AuthorsHakim, M. / Fass, D.
CitationJournal: J.Virol. / Year: 2011
Title: Structure of a baculovirus sulfhydryl oxidase, a highly divergent member of the erv flavoenzyme family.
Authors: Hakim, M. / Mandelbaum, A. / Fass, D.
History
DepositionSep 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: sulfhydryl oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5974
Polymers31,6831
Non-polymers9143
Water3,513195
1
A: sulfhydryl oxidase
hetero molecules

A: sulfhydryl oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1938
Polymers63,3662
Non-polymers1,8276
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7360 Å2
ΔGint-22 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.765, 80.839, 65.053
Angle α, β, γ (deg.)90.00, 105.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-299-

HOH

21A-329-

HOH

31A-385-

HOH

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Components

#1: Protein sulfhydryl oxidase / 33 kDa early protein homolog / p33


Mass: 31682.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Autographa californica nucleopolyhedrovirus
Gene: Ac92, P33 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P41480, thiol oxidase
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 0.1 M acetic acid, 50 mM arginine-HCl, 750 mM NaCl, 5% ethanol, 24% PEG 5000-MME, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97692 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2010
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelengthWavelength: 0.97692 Å / Relative weight: 1
ReflectionResolution: 1.47→50 Å / Num. obs: 46687 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rsym value: 0.069 / Net I/σ(I): 19.2
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.54 / Num. unique all: 2322 / Rsym value: 1 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIXmodel building
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.47→50 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2335 3259 RANDOM
Rwork0.208 --
obs-46375 -
Refinement stepCycle: LAST / Resolution: 1.47→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2160 0 62 195 2417
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00538
X-RAY DIFFRACTIONc_angle_deg0.95014
LS refinement shellResolution: 1.47→1.48 Å
RfactorNum. reflection
Rfree0.3317 55
Rwork0.3316 -
obs-821

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