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Yorodumi- PDB-5k90: Crystal structure of dimeric chlorite dismutase from Cyanothece s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5k90 | ||||||
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Title | Crystal structure of dimeric chlorite dismutase from Cyanothece sp. PCC7425 in complex with isothiocyanate | ||||||
Components | Chlorite dismutase | ||||||
Keywords | OXIDOREDUCTASE / chlorite dismutase / cyanobacteria / heme / ferredoxin-like fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cyanothece sp. | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å | ||||||
Authors | Puehringer, D. / Schaffner, I. / Mlynek, G. / Obinger, C. / Djinovic-Carugo, K. | ||||||
Citation | Journal: ACS Catal / Year: 2017 Title: Molecular Mechanism of Enzymatic Chlorite Detoxification: Insights from Structural and Kinetic Studies. Authors: Schaffner, I. / Mlynek, G. / Flego, N. / Puhringer, D. / Libiseller-Egger, J. / Coates, L. / Hofbauer, S. / Bellei, M. / Furtmuller, P.G. / Battistuzzi, G. / Smulevich, G. / Djinovic-Carugo, K. / Obinger, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5k90.cif.gz | 471.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k90.ent.gz | 397.5 KB | Display | PDB format |
PDBx/mmJSON format | 5k90.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5k90_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 5k90_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 5k90_validation.xml.gz | 39.5 KB | Display | |
Data in CIF | 5k90_validation.cif.gz | 56.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/5k90 ftp://data.pdbj.org/pub/pdb/validation_reports/k9/5k90 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 21830.881 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cyanothece sp. (strain PCC 7425 / ATCC 29141) (bacteria) Strain: PCC 7425 / ATCC 29141 / Gene: Cyan7425_1434 / Details (production host): pET-52b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: B8HNS6 |
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-Non-polymers , 6 types, 821 molecules
#2: Chemical | ChemComp-IS8 / #3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
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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: 3.04 Å3/Da / Density % sol: 59.6 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.15 M MgSO4, 0.1 M MES pH 6.5, 25% (w/v) PEG3350, 10 mM NaSCN |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.7749 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2015 Details: Kirkpatrick Baez bimorph mirror pair for horizontal and vertical focussing |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7749 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→46.775 Å / Num. obs: 242310 / % possible obs: 93 % / Redundancy: 1.8 % / Biso Wilson estimate: 14.08 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.07663 / Net I/σ(I): 4.99 |
Reflection shell | Resolution: 1.28→1.326 Å / Redundancy: 1.8 % / Rmerge(I) obs: 2.588 / Mean I/σ(I) obs: 0.27 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.28→46.775 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 37.06 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.79 Å2 / Biso mean: 28.0031 Å2 / Biso min: 12.01 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.28→46.775 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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