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Yorodumi- PDB-6ebc: OhrB (Organic Hydroperoxide Resistance protein) wild type from Ch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ebc | ||||||
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Title | OhrB (Organic Hydroperoxide Resistance protein) wild type from Chromobacterium violaceum and reduced by DTT | ||||||
Components | Organic hydroperoxide resistance protein | ||||||
Keywords | OXIDOREDUCTASE / Ohr / thiol-proxidase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Chromobacterium violaceum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 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 | 6ebc.cif.gz | 225.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ebc.ent.gz | 181.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ebc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ebc_validation.pdf.gz | 484 KB | Display | wwPDB validaton report |
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Full document | 6ebc_full_validation.pdf.gz | 493.4 KB | Display | |
Data in XML | 6ebc_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 6ebc_validation.cif.gz | 35.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/6ebc ftp://data.pdbj.org/pub/pdb/validation_reports/eb/6ebc | HTTPS FTP |
-Related structure data
Related structure data | 6eb4SC 6ebdC 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: _ / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 16852.906 Da / Num. of mol.: 4 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 | ChemComp-CL / #3: Chemical | #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: 2.83 Å3/Da / Density % sol: 56.5 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: Purified protein 10mg/ml in 5mM Tris-Hcl, pH 7.4 and DTT 10mM Crystallization solution: Magnesium Chloride 200mM, BIS-TRIS 100mM pH 5.5, PEG 3,350 25%w/v Then, Soaked with Cs + DTT 50mM |
-Data collection
Diffraction | Mean temperature: 273.15 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.45866 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.45866 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→45.49 Å / Num. obs: 61621 / % possible obs: 100 % / Redundancy: 17.2 % / CC1/2: 0.999 / Rpim(I) all: 0.038 / Rrim(I) all: 0.114 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.87→1.91 Å / Redundancy: 9.3 % / Num. unique obs: 3977 / CC1/2: 0.356 / Rpim(I) all: 1.275 / Rrim(I) all: 2.798 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EB4 Resolution: 1.87→35 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 7.02 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.112 / 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: 40.783 Å2
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Refinement step | Cycle: 1 / Resolution: 1.87→35 Å
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Refine LS restraints |
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