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- PDB-4u4i: Megavirus chilensis superoxide dismutase -

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Basic information

Entry
Database: PDB / ID: 4u4i
TitleMegavirus chilensis superoxide dismutase
ComponentsCu/Zn superoxide dismutase
KeywordsOXIDOREDUCTASE / Cu-Zn Superoxide dismutase / metal-free
Function / homology
Function and homology information


superoxide metabolic process / copper ion binding
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Superoxide dismutase Cu-Zn
Similarity search - Component
Biological speciesMegavirus chiliensis
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsLartigue, A. / Claverie, J.-M. / Burlat, B. / Coutard, B. / Abergel, C.
Citation
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.
History
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
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,6172
Polymers35,6172
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint0 kcal/mol
Surface area11910 Å2
MethodPISA
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

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Components

#1: Protein Cu/Zn superoxide dismutase


Mass: 17808.688 Da / Num. of mol.: 2 / Mutation: M1GPGS
Source method: isolated from a genetically manipulated source
Details: Environmental chile / Source: (gene. exp.) Megavirus chiliensis / 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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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

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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

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
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
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091980
X-RAY DIFFRACTIONf_angle_d1.1392671
X-RAY DIFFRACTIONf_dihedral_angle_d14.254719
X-RAY DIFFRACTIONf_chiral_restr0.053289
X-RAY DIFFRACTIONf_plane_restr0.005354
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.2-2.2710.27671400.2091263
2.271-2.35220.25681400.18861256
2.3522-2.44640.22011390.18621255
2.4464-2.55770.23311400.19481255
2.5577-2.69250.27171410.20691270
2.6925-2.86110.26141410.19481270
2.8611-3.0820.26381420.18821270
3.082-3.39190.2321420.17751283
3.3919-3.88230.19341440.17631293
3.8823-4.88970.18841470.16421323
4.8897-38.04610.23141570.20281415

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