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- PDB-3gwn: Crystal structure of the FAD binding domain from mimivirus sulfhy... -

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Basic information

Entry
Database: PDB / ID: 3gwn
TitleCrystal structure of the FAD binding domain from mimivirus sulfhydryl oxidase R596
ComponentsProbable FAD-linked sulfhydryl oxidase R596
KeywordsOXIDOREDUCTASE / FIVE HELIX BUNDLE / HOMODIMER / Disulfide bond / FAD / Flavoprotein / Virion
Function / homology
Function and homology information


flavin-dependent sulfhydryl oxidase activity / thiol oxidase / virion component / flavin adenine dinucleotide binding
Similarity search - Function
: / Mimivirus sulfhydryl oxidase R596-like, C-terminal domain / 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 / Probable FAD-linked sulfhydryl oxidase R596
Similarity search - Component
Biological speciesAcanthamoeba polyphaga mimivirus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 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: Non-polymer description / Version format compliance
Revision 1.2Dec 7, 2016Group: Database references
Revision 1.3Nov 1, 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 1.4Nov 20, 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: Probable FAD-linked sulfhydryl oxidase R596
B: Probable FAD-linked sulfhydryl oxidase R596
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5458
Polymers26,5942
Non-polymers1,9516
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-32 kcal/mol
Surface area11990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.166, 58.584, 119.085
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 Probable FAD-linked sulfhydryl oxidase R596


Mass: 13297.046 Da / Num. of mol.: 2 / Fragment: mimivirus R596 FAD binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: MIMI_R596, R596 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) plysS / References: UniProt: Q5UP54, 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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.5M ammonium sulfate, 25% PEG 4K, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. all: 24453 / Num. obs: 24259 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Biso Wilson estimate: 22.8 Å2 / Rsym value: 0.078 / Net I/σ(I): 12.5
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.407 / % possible all: 97.9

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Processing

Software
NameClassification
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JR8

1jr8


Resolution: 1.78→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1533 -RANDOM
Rwork0.181 ---
all-24453 --
obs-24196 98.9 %-
Refinement stepCycle: LAST / Resolution: 1.78→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1862 0 127 229 2218
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.005
X-RAY DIFFRACTIONc_angle_deg2.125

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