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- PDB-4u4i: Megavirus chilensis superoxide dismutase -

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Basic information

Database: PDB / ID: 4u4i
TitleMegavirus chilensis superoxide dismutase
ComponentsCu/Zn superoxide dismutase
KeywordsOXIDOREDUCTASE / Cu-Zn Superoxide dismutase / metal-free
Function / homologySuperoxide dismutase, copper/zinc binding domain / Superoxide dismutase, copper/zinc, binding site / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase-like, copper/zinc binding domain superfamily / Copper/zinc superoxide dismutase (SODC) / Copper/Zinc superoxide dismutase signature 2. / superoxide dismutase activity / metal ion binding / Cu/Zn superoxide dismutase
Function and homology information
Biological speciesMegavirus chiliensis
AuthorsLartigue, A. / Claverie, J.-M. / Burlat, B. / Coutard, B. / Abergel, C.
Journal: J.Virol. / Year: 2015
Title: The megavirus chilensis cu,zn-superoxide dismutase: the first viral structure of a typical cellular copper chaperone-independent hyperstable dimeric enzyme.
Authors: Lartigue, A. / Burlat, B. / Coutard, B. / Chaspoul, F. / Claverie, J.M. / Abergel, C.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2012

Title: Preliminary crystallographic analysis of the Megavirus superoxide dismutase.
Authors: Lartigue, A. / Philippe, N. / Jeudy, S. / Abergel, C.
Validation Report
SummaryFull reportAbout validation report
DepositionJul 23, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references

Structure visualization

Structure viewerMolecule:

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Deposited unit
A: Cu/Zn superoxide dismutase
B: Cu/Zn superoxide dismutase

Theoretical massNumber of molelcules
Total (without water)35,6172

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint0 kcal/mol
Surface area11910 Å2
Unit cell
Length a, b, c (Å)70.626, 70.626, 117.426
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212


#1: Protein/peptide Cu/Zn superoxide dismutase

Mass: 17808.688 Da / Num. of mol.: 2
Details: The loops involved in copper and Zinc binding are disrdered in the crystal structure
Mutation: M1GPGS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Megavirus chiliensis / Details: Environmental chile / Gene: mg277 / Plasmid: modified pETDuet
Details (production host): human rhinovirus 3C protease cleavage site inserted
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: G5CS11, superoxide dismutase
#2: Water ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O / Water

Experimental details


ExperimentMethod: X-RAY DIFFRACTION

Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 40.55 % / Description: rods
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M sodium acetate buffer, 20%(w/v) PEG 4000, 20%(v/v) MPD
PH range: 5.5

Data collection

DiffractionMean temperature: 105 K
Ambient temp details: oscillation angle 0.5, distance 291.72mm, 380 images
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9792 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→39.14 Å / Num. obs: 15785 / % possible obs: 100 % / Redundancy: 14.9 % / Biso Wilson estimate: 33.83 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.3
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 15 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1 / % possible all: 100


PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→38.04 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 1573 10 %Random selection
Rwork0.1857 ---
Obs0.1897 15726 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.6 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1933 0 0 107 2040
Refine LS restraints


TypeDev idealNumber
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION / % reflection Rfree: 11 % / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork

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