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Yorodumi- PDB-6ebd: OhrB (Organic Hydroperoxide Resistance protein) mutant (C60A) fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ebd | ||||||
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Title | OhrB (Organic Hydroperoxide Resistance protein) mutant (C60A) from Chromobacterium violaceum, interacting with dihydrolipoamide | ||||||
Components | Organic hydroperoxide resistance protein | ||||||
Keywords | OXIDOREDUCTASE / Ohr / thiol-proxidase / Dihydrolipoamide | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Chromobacterium violaceum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å | ||||||
Authors | Domingos, R.M. / Teixeira, R.D. / Alegria, T.G.P. / Vieira, P.S. / Murakami, M.T. / Netto, L.E.S. | ||||||
Funding support | Brazil, 1items
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Citation | Journal: Acs Catalysis / Year: 2020 Title: Substrate and product-assisted catalysis: molecular aspects behind structural switches along Organic Hydroperoxide Resistance Protein catalytic cycle Authors: Domingos, R.M. / Teixeira, R.D. / Zeida, A. / Agudelo, W.A. / Alegria, T.G.P. / da Silva Neto, J.F. / Vieira, P.S. / Murakami, M.T. / Farah, C.S. / Estrin, D.A. / Netto, L.E.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ebd.cif.gz | 223.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ebd.ent.gz | 181.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ebd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ebd_validation.pdf.gz | 473.6 KB | Display | wwPDB validaton report |
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Full document | 6ebd_full_validation.pdf.gz | 478.2 KB | Display | |
Data in XML | 6ebd_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 6ebd_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/6ebd ftp://data.pdbj.org/pub/pdb/validation_reports/eb/6ebd | HTTPS FTP |
-Related structure data
Related structure data | 6eb4SC 6ebcC 6ebgC 6ecyC 6ed0C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 16820.842 Da / Num. of mol.: 4 / Mutation: C60A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Gene: CBW21_15220 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A202B6V5 #2: Chemical | #3: Chemical | ChemComp-CL / #4: 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: 2.96 Å3/Da / Density % sol: 62.71 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Purified Ohr_C60A protein 10mg/ml in 5mM Tris-Hcl pH 7.4 Crystallisation conditions: Magnesium Clhoride 200mM, BIS-TRIS 100mM pH 5.5, PEG 3,350 25%w/v crystal was soaked for 10min in ...Details: Purified Ohr_C60A protein 10mg/ml in 5mM Tris-Hcl pH 7.4 Crystallisation conditions: Magnesium Clhoride 200mM, BIS-TRIS 100mM pH 5.5, PEG 3,350 25%w/v crystal was soaked for 10min in Lipoamide 5mM, solved in 5% ethanol and Crystallisation condition |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.61→43.84 Å / Num. obs: 23763 / % possible obs: 99.9 % / Redundancy: 20.8 % / CC1/2: 1 / Rpim(I) all: 0.105 / Rrim(I) all: 0.343 / Net I/σ(I): 10.82 |
Reflection shell | Resolution: 2.61→2.73 Å / Num. unique obs: 60434 / CC1/2: 0.41 / Rpim(I) all: 1.526 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EB4 Resolution: 2.61→35 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 32.481 / SU ML: 0.278 / Cross valid method: THROUGHOUT / ESU R: 0.436 / ESU R Free: 0.266 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.207 Å2
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Refinement step | Cycle: 1 / Resolution: 2.61→35 Å
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Refine LS restraints |
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