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

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Basic information

Entry
Database: PDB / ID: 3qzy
TitleStructure of Baculovirus Sulfhydryl Oxidase Ac92
ComponentsBaculovirus sulfhydryl oxidase Ac92
KeywordsOXIDOREDUCTASE / flavin adenine dinucleotide / viral protein / 4-helix bundle / 5-helix bundle / sulfhydryl oxidase / nucleus
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
FLAVIN-ADENINE DINUCLEOTIDE / IMIDAZOLE / PHOSPHATE ION / FAD-linked sulfhydryl oxidase
Similarity search - Component
Biological speciesAutographa californica nucleopolyhedrovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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
DepositionMar 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Baculovirus sulfhydryl oxidase Ac92
B: Baculovirus sulfhydryl oxidase Ac92
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8567
Polymers62,0262
Non-polymers1,8305
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-30 kcal/mol
Surface area23020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.730, 50.730, 65.170
Angle α, β, γ (deg.)83.95, 79.01, 65.58
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Baculovirus sulfhydryl oxidase Ac92 / p33


Mass: 31013.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Autographa californica nucleopolyhedrovirus
Gene: Ac92, P33 / Plasmid: pET28 / 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.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 4% PEG 2000 MME, 7% DMSO, 0.1M bicine, 0.05M arginine-HCl, 0.001M ZnCl2, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97692 Å
DetectorType: ADSC Q315R / Detector: CCD / Date: Jun 22, 2010
RadiationMonochromator: Synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97692 Å / Relative weight: 1
ReflectionResolution: 2.14→40.34 Å / Num. all: 31279 / Num. obs: 31279 / % possible obs: 97.6 % / Redundancy: 3.8 % / Rsym value: 0.075 / Net I/σ(I): 8.5
Reflection shellResolution: 2.14→2.26 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 4477 / Rsym value: 0.399 / % possible all: 95.7

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3P0K

3p0k


Resolution: 2.14→40.34 Å / σ(F): 2 / Stereochemistry target values: CNS
RfactorNum. reflectionSelection details
Rfree0.2698 2183 RANDOM
Rwork0.2305 --
all-32036 -
obs-31277 -
Refinement stepCycle: LAST / Resolution: 2.14→40.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4097 0 121 138 4356
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00739
X-RAY DIFFRACTIONc_angle_deg1.04432
LS refinement shellResolution: 2.14→2.16 Å / Rfactor Rfree: 0.3183 / Rfactor Rwork: 0.2698

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