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Yorodumi- PDB-5u63: Crystal structure of putative thioredoxin reductase from Haemophi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u63 | ||||||
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Title | Crystal structure of putative thioredoxin reductase from Haemophilus influenzae | ||||||
Components | Thioredoxin reductase | ||||||
Keywords | LYASE / cofactor / nucleotide / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / cytoplasm Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Michalska, K. / Maltseva, N. / Mulligan, R. / Grimshaw, S. / Joachimiak, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of putative thioredoxin reductase from Haemophilus influenzae Authors: Michalska, K. / Maltseva, N. / Mulligan, R. / Grimshaw, S. / Joachimiak, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u63.cif.gz | 271.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u63.ent.gz | 218.2 KB | Display | PDB format |
PDBx/mmJSON format | 5u63.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u6/5u63 ftp://data.pdbj.org/pub/pdb/validation_reports/u6/5u63 | HTTPS FTP |
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-Related structure data
Related structure data | 1tdeS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | THE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 34705.066 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria) Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: trxB, HI_1158 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Magic References: UniProt: P43788, thioredoxin-disulfide reductase |
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-Non-polymers , 6 types, 372 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-NA / | #7: 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: 2.56 Å3/Da / Density % sol: 51.95 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.16 M Mg acetate, 0.08 M Na cacodylate, pH 6.5, 16% PEG 8K, 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2016 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→30 Å / Num. obs: 49269 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 25 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 25.52 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 20.2 % / Rmerge(I) obs: 1.117 / Mean I/σ(I) obs: 2.46 / CC1/2: 0.754 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TDE Resolution: 1.99→29.759 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.55 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→29.759 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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