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Yorodumi- PDB-3zit: Crystal structure of the thioredoxin-like protein BC3987 mutant T8A -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zit | ||||||
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Title | Crystal structure of the thioredoxin-like protein BC3987 mutant T8A | ||||||
Components | THIOREDOXIN | ||||||
Keywords | OXIDOREDUCTASE / GLUTAREDOXIN / TRX / GRX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | BACILLUS CEREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å | ||||||
Authors | Rohr, A.K. / Hammerstad, M. / Andersson, K.K. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Tuning of Thioredoxin Redox Properties by Intramolecular Hydrogen Bonds. Authors: Rohr, A.K. / Hammerstad, M. / Andersson, K.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zit.cif.gz | 78.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zit.ent.gz | 59.5 KB | Display | PDB format |
PDBx/mmJSON format | 3zit.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/3zit ftp://data.pdbj.org/pub/pdb/validation_reports/zi/3zit | HTTPS FTP |
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-Related structure data
Related structure data | 3zijSC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8975.234 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS CEREUS (bacteria) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q819J1 #2: 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: 1.72 Å3/Da / Density % sol: 28 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.1 M HEPES PH 7.5, 50 MM MGCL2 AND 30 % (W/V) POLYETHYLENE GLYCOL MONOMETHYL ETHER 550 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976273 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976273 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→24.78 Å / Num. obs: 31318 / % possible obs: 84.9 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.18→1.25 Å / Redundancy: 3 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4.9 / % possible all: 83.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZIJ Resolution: 1.18→24.78 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.198 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.052 / 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: 20.814 Å2
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Refinement step | Cycle: LAST / Resolution: 1.18→24.78 Å
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Refine LS restraints |
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