+Open data
-Basic information
Entry | Database: PDB / ID: 3zij | ||||||
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Title | Crystal structure of the thioredoxin-like protein BC3987 | ||||||
Components | THIOREDOXIN | ||||||
Keywords | OXIDOREDUCTASE / GLUTAREDOXIN / DISULFIDE / TRX / GRX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | BACILLUS CEREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 | 3zij.cif.gz | 44.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zij.ent.gz | 31.5 KB | Display | PDB format |
PDBx/mmJSON format | 3zij.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zij_validation.pdf.gz | 430.4 KB | Display | wwPDB validaton report |
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Full document | 3zij_full_validation.pdf.gz | 432.1 KB | Display | |
Data in XML | 3zij_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 3zij_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/3zij ftp://data.pdbj.org/pub/pdb/validation_reports/zi/3zij | HTTPS FTP |
-Related structure data
Related structure data | 3zitC 1r7hS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 9005.260 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS CEREUS (bacteria) / 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: 1.4 Å3/Da / Density % sol: 29 % / 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: 0.975948 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975948 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→33 Å / Num. obs: 22238 / % possible obs: 94.3 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 6.1 / % possible all: 93.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1R7H Resolution: 1.4→32.98 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.318 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.075 / 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: 19.879 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→32.98 Å
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Refine LS restraints |
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