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- PDB-2q2l: Crystal Structure of Superoxide Dismutase from P. atrosanguina -

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Basic information

Entry
Database: PDB / ID: 2q2l
TitleCrystal Structure of Superoxide Dismutase from P. atrosanguina
ComponentsSuperoxide Dismutase
KeywordsOXIDOREDUCTASE / SOD / SAD / Antioxidant / Metal-Binding
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / Copper/Zinc superoxide dismutase signature 1. / 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 (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesPotentilla atrosanguinea (plant)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.367 Å
AuthorsManickam, Y. / Gill, J. / Mishra, P.C. / Sharma, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: SAD phasing of a structure based on cocrystallized iodides using an in-house Cu Kalpha X-ray source: effects of data redundancy and completeness on structure solution
Authors: Yogavel, M. / Gill, J. / Mishra, P.C. / Sharma, A.
History
DepositionMay 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Superoxide Dismutase
B: Superoxide Dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,83214
Polymers30,4322
Non-polymers1,40012
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-13 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.14, 64.12, 63.62
Angle α, β, γ (deg.)90.00, 124.33, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2034-

HOH

21B-2048-

HOH

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Components

#1: Protein Superoxide Dismutase / E.C.1.15.1.1 / copper-zinc superoxide dismutase


Mass: 15215.869 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Potentilla atrosanguinea (plant) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M50 / References: UniProt: B2CP37*PLUS, superoxide dismutase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.47 Å3/Da / Density % sol: 50.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 3350, 0.2 M Ammonium Iodide, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 19, 2006 / Details: Osmic mirrors (Vari Max HR)
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.367→50 Å / Num. all: 11646 / Num. obs: 10953 / % possible obs: 94.4 % / Observed criterion σ(I): 1 / Redundancy: 6.3 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 32.7
Reflection shellResolution: 2.367→2.428 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 6 / % possible all: 63.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SOLVEphasing
REFMAC5.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.367→50 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.234 546 -random
Rwork0.167 ---
all0.173 11646 --
obs-10953 94.27 %-
Refinement stepCycle: LAST / Resolution: 2.367→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2184 0 12 203 2399
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.026
X-RAY DIFFRACTIONr_angle_refined_deg2.427

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