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Yorodumi- PDB-2wwn: Yersinia pseudotuberculosis Superoxide Dismutase C with bound Azide -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wwn | |||||||||
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Title | Yersinia pseudotuberculosis Superoxide Dismutase C with bound Azide | |||||||||
Components | SUPEROXIDE DISMUTASE [CU-ZN] | |||||||||
Keywords | OXIDOREDUCTASE / METAL-BINDING | |||||||||
Function / homology | Function and homology information superoxide dismutase / superoxide dismutase activity / periplasmic space / copper ion binding / extracellular space Similarity search - Function | |||||||||
Biological species | YERSINIA PSEUDOTUBERCULOSIS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Basak, A.K. / Duffield, M.L. / Naylor, C.E. / Huyet, J. / Titball, R.W. | |||||||||
Citation | Journal: To be Published Title: Crystal Structure of the Yersinia Pseudotuberculosis Superoxide Dismutase (Sodc) Authors: Huyet, J. / Naylor, C.E. / Titball, R.W. / Bullifent, H. / Walker, N. / Jones, H.E. / Duffied, M.L. / Basak, A.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wwn.cif.gz | 129.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wwn.ent.gz | 100.1 KB | Display | PDB format |
PDBx/mmJSON format | 2wwn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wwn_validation.pdf.gz | 453.4 KB | Display | wwPDB validaton report |
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Full document | 2wwn_full_validation.pdf.gz | 455.1 KB | Display | |
Data in XML | 2wwn_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 2wwn_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/2wwn ftp://data.pdbj.org/pub/pdb/validation_reports/ww/2wwn | HTTPS FTP |
-Related structure data
Related structure data | 2wwoC 1esoS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (0.40183, -0.67247, -0.62154), Vector: |
-Components
#1: Protein | Mass: 17371.846 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) YERSINIA PSEUDOTUBERCULOSIS (bacteria) / Strain: IP32953 / Plasmid: PGEX-6P / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): STAR / References: UniProt: Q66ED7, superoxide dismutase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-MES / | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | SEQUENCE CONTAINS SIGNAL PEPTIDE NOT PRESENT IN MATURE PROTEIN | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.1M MES-NAOH, PH 6.5, 0.2M ZNSO4, 25% PEG-MME 550, 10MM NA AZIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0332 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 5, 2008 / Details: MIRRORS |
Radiation | Monochromator: SILICON (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 13914 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2→2.74 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ESO Resolution: 2.6→41.812 Å / SU ML: 0.46 / σ(F): 1.95 / Phase error: 21.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.741 Å2 / ksol: 0.321 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→41.812 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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