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- PDB-3kbf: C. elegans Cu,Zn Superoxide Dismutase -

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Basic information

Entry
Database: PDB / ID: 3kbf
TitleC. elegans Cu,Zn Superoxide Dismutase
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / cu-zn superoxide dismutase / antioxidant / nematode / Disulfide bond / Metal-binding
Function / homology
Function and homology information


Detoxification of Reactive Oxygen Species / Platelet degranulation / regulation of vulval development / regulation of brood size / superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / copper ion binding / protein homodimerization activity ...Detoxification of Reactive Oxygen Species / Platelet degranulation / regulation of vulval development / regulation of brood size / superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / copper ion binding / protein homodimerization activity / mitochondrion / cytosol / cytoplasm
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 / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsPakhomova, O.N. / Taylor, A.B. / Schuermann, J.P. / Culotta, V.L. / Hart, P.J.
CitationJournal: To be Published
Title: X-ray Crystal Structure of C. elegans Cu,Zn Superoxide Dismutase
Authors: Pakhomova, O.N. / Taylor, A.B. / Schuermann, J.P. / Culotta, V.L. / Hart, P.J.
History
DepositionOct 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: 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 [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3524
Polymers16,1271
Non-polymers2253
Water3,981221
1
A: Superoxide dismutase [Cu-Zn]
hetero molecules

A: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7048
Polymers32,2542
Non-polymers4506
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area2060 Å2
ΔGint-60 kcal/mol
Surface area14430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.204, 68.986, 110.488
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Superoxide dismutase [Cu-Zn]


Mass: 16126.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: C15F1.7, sod-1 / Plasmid: pAED4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P34697, superoxide dismutase
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 100 mM MES, 65% MPD, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 36429 / % possible obs: 97.6 % / Redundancy: 11.9 % / Biso Wilson estimate: 13.2 Å2 / Rsym value: 0.055 / Net I/σ(I): 35.4
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 2989 / Rsym value: 0.364 / % possible all: 81.8

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→32.926 Å / SU ML: 0.13 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1592 1828 5.03 %random
Rwork0.1466 ---
obs0.1473 36365 97.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.296 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso mean: 20.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.3026 Å20 Å20 Å2
2---3.1506 Å20 Å2
3---0.848 Å2
Refinement stepCycle: LAST / Resolution: 1.3→32.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1123 0 7 221 1351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061171
X-RAY DIFFRACTIONf_angle_d1.0141592
X-RAY DIFFRACTIONf_dihedral_angle_d15.047419
X-RAY DIFFRACTIONf_chiral_restr0.066182
X-RAY DIFFRACTIONf_plane_restr0.004211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.33460.22081080.17792051X-RAY DIFFRACTION76
1.3346-1.37390.17151120.15372521X-RAY DIFFRACTION93
1.3739-1.41820.18021510.12782641X-RAY DIFFRACTION98
1.4182-1.46890.16541300.11822691X-RAY DIFFRACTION99
1.4689-1.52770.15671310.11382712X-RAY DIFFRACTION100
1.5277-1.59720.13851320.10892688X-RAY DIFFRACTION100
1.5972-1.68150.14011510.11492689X-RAY DIFFRACTION100
1.6815-1.78680.12711620.11132720X-RAY DIFFRACTION100
1.7868-1.92470.12711520.10912690X-RAY DIFFRACTION100
1.9247-2.11840.13181480.12082728X-RAY DIFFRACTION100
2.1184-2.42490.1731310.13692765X-RAY DIFFRACTION100
2.4249-3.05470.17021500.16232782X-RAY DIFFRACTION100
3.0547-32.93640.15451700.16452859X-RAY DIFFRACTION100

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