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- PDB-3gwl: Crystal structure of ASFV pB119L, a viral sulfhydryl oxidase -

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Basic information

Entry
Database: PDB / ID: 3gwl
TitleCrystal structure of ASFV pB119L, a viral sulfhydryl oxidase
ComponentsFAD-linked sulfhydryl oxidase
KeywordsOXIDOREDUCTASE / HOMODIMER / FIVE-HELIX BUNDLE / Disulfide bond / FAD / Flavoprotein / Late protein / Virulence
Function / homology
Function and homology information


flavin-dependent sulfhydryl oxidase activity / thiol oxidase / virion component => GO:0044423 / : / host cell cytoplasm
Similarity search - Function
Sulfhydryl oxidase ALR/ERV / ERV/ALR sulfhydryl oxidase domain / ERV/ALR sulfhydryl oxidase domain / ERV/ALR sulfhydryl oxidase domain superfamily / Erv1 / Alr family / ERV/ALR sulfhydryl oxidase domain profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FAD-linked sulfhydryl oxidase
Similarity search - Component
Biological speciesAfrican swine fever virus BA71V
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.1 Å
AuthorsHakim, M. / Fass, D.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Dimer interface migration in a viral sulfhydryl oxidase
Authors: Hakim, M. / Fass, D.
History
DepositionApr 1, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 7, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FAD-linked sulfhydryl oxidase
B: FAD-linked sulfhydryl oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3844
Polymers25,8132
Non-polymers1,5712
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-15 kcal/mol
Surface area11900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.450, 69.000, 83.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FAD-linked sulfhydryl oxidase / p14


Mass: 12906.607 Da / Num. of mol.: 2 / Fragment: UNP residues 1-103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus BA71V / Strain: Badajoz 1971 Vero-adapted, BA71V / Gene: 9GL, B119L, Ba71V-073 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) plysS / References: UniProt: Q65163, thiol oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1M HEPES (pH 7.8), 7% (v/v) isopropanol, 5% (w/v) PEG 12K, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 20, 2007 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 16345 / Num. obs: 16153 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 28 Å2 / Rsym value: 0.074 / Net I/σ(I): 13.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 5.1 / Rsym value: 0.322 / % possible all: 100

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1103 -RANDOM
Rwork0.218 ---
all-16345 --
obs-16030 98.1 %-
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 106 177 2085
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg2.13

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