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- PDB-3td7: Crysal structure of the mimivirus sulfhydryl oxidase R596 -

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Basic information

Entry
Database: PDB / ID: 3td7
TitleCrysal structure of the mimivirus sulfhydryl oxidase R596
ComponentsFAD-linked sulfhydryl oxidase R596
KeywordsOXIDOREDUCTASE / four helix-bundle / ORFan domain / Oxidase
Function / homology
Function and homology information


flavin-dependent sulfhydryl oxidase activity / thiol oxidase / virion component
Similarity search - Function
Sulfhydryl oxidase R596, ORFan domain / : / 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) ...Sulfhydryl oxidase R596, ORFan domain / : / 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 / SYNCHROTRON / MAD / Resolution: 2.21 Å
AuthorsHakim, M. / Fass, D.
CitationJournal: Plos One / Year: 2012
Title: Exploring ORFan domains in giant viruses: structure of mimivirus sulfhydryl oxidase R596.
Authors: Hakim, M. / Ezerina, D. / Alon, A. / Vonshak, O. / Fass, D.
History
DepositionAug 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FAD-linked sulfhydryl oxidase R596
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9882
Polymers34,2031
Non-polymers7861
Water2,198122
1
A: FAD-linked sulfhydryl oxidase R596
hetero molecules

A: FAD-linked sulfhydryl oxidase R596
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9774
Polymers68,4062
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area7730 Å2
ΔGint-64 kcal/mol
Surface area24430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.306, 91.306, 200.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein FAD-linked sulfhydryl oxidase R596


Mass: 34202.867 Da / Num. of mol.: 1 / Mutation: C23A, C201A, C229A, C266A
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 / References: UniProt: Q5UP54, thiol oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.5365.18
2
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES, 200 mM magnesium chloride, 200 mM lithium sulfate, 5% (v/v) 2-methyl-2,4-pentanediol (MPD), and 15-20% (w/v) PEG 1500, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9766 Å
DetectorType: Pilatus 6M / Detector: PIXEL / Date: May 29, 2011
RadiationMonochromator: Si(311) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9766 Å / Relative weight: 1
ReflectionResolution: 2.21→45 Å / Num. all: 25626 / Num. obs: 25063 / % possible obs: 97.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 19.3 % / Rsym value: 0.1 / Net I/σ(I): 18.9
Reflection shellResolution: 2.21→2.33 Å / Redundancy: 19.2 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 3431 / Rsym value: 0.743 / % possible all: 93.6

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Processing

Software
NameVersionClassification
EDNAdata collection
PHENIXmodel building
CNS1.2refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.21→45 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.253 1718 RANDOM
Rwork0.227 --
all-25047 -
obs-23329 -
Refinement stepCycle: LAST / Resolution: 2.21→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2085 0 53 122 2260
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.07852
X-RAY DIFFRACTIONc_bond_d0.006669

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