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- PDB-6ed0: OhrA (Organic Hydroperoxide Resistance protein) mutant (C61S) in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ed0 | ||||||
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Title | OhrA (Organic Hydroperoxide Resistance protein) mutant (C61S) in the "open conformation" from chromobacterium violaceum | ||||||
![]() | Organic hydroperoxide resistance protein | ||||||
![]() | OXIDOREDUCTASE / Ohr / thiol-proxidase | ||||||
Function / homology | Organic hydroperoxide resistance protein famiy / OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / K homology domain-like, alpha/beta / response to oxidative stress / Organic hydroperoxide resistance protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Domingos, R.M. / Teixeira, R.D. / Alegria, T.G.P. / Netto, L.E.S. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119.8 KB | Display | ![]() |
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PDB format | ![]() | 92.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.6 KB | Display | ![]() |
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Full document | ![]() | 449.5 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 17.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6eb4C ![]() 6ebcC ![]() 6ebdC ![]() 6ebgC ![]() 6ecySC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 1 - 141 / Label seq-ID: 21 - 161
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Components
#1: Protein | Mass: 16600.633 Da / Num. of mol.: 2 / Mutation: C61S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757 Gene: ohr2, CV_0209 / Production host: ![]() ![]() #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.99 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: purified ohr protein at 10mg/ml in 5mM Tris-Hcl, pH 7.4 & 50mM NaCl) Crystallisation conditions: Ammonium sulfate 200mM, Sodium acetate 100mM pH 4, PEG 2,000 30%w/v |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→36.34 Å / Num. obs: 43151 / % possible obs: 97.9 % / Redundancy: 10.1 % / CC1/2: 1 / Rpim(I) all: 0.017 / Rrim(I) all: 0.038 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 1.44→1.47 Å / Redundancy: 8.3 % / Num. unique obs: 1879 / CC1/2: 0.547 / Rpim(I) all: 1.261 / Rrim(I) all: 2.629 / % possible all: 84.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6ECY Resolution: 1.44→35 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.564 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.914 Å2
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Refinement step | Cycle: 1 / Resolution: 1.44→35 Å
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Refine LS restraints |
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