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Yorodumi- PDB-5utx: Crystal structure of thioredoxin-disulfide reductase from Vibrio ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5utx | ||||||
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Title | Crystal structure of thioredoxin-disulfide reductase from Vibrio vulnificus CMCP6 - apo form | ||||||
Components | Thioredoxin reductase | ||||||
Keywords | OXIDOREDUCTASE / Structural Genomics / Center For Structural Genomics Of Infectious Diseases / CSGID / thioredoxin-disulfide reductase | ||||||
Function / homology | Function and homology information thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | Vibrio vulnificus CMCP6 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å | ||||||
Authors | Chang, C. / Grimshaw, S. / Maltseva, N. / Mulligan, R. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: Crystal structure of thioredoxin-disulfide reductase from Vibrio vulnificus CMCP6 - apo form Authors: Chang, C. / Grimshaw, S. / Maltseva, N. / Mulligan, R. / Anderson, W.F. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5utx.cif.gz | 231.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5utx.ent.gz | 184.5 KB | Display | PDB format |
PDBx/mmJSON format | 5utx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5utx_validation.pdf.gz | 449.4 KB | Display | wwPDB validaton report |
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Full document | 5utx_full_validation.pdf.gz | 453.6 KB | Display | |
Data in XML | 5utx_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 5utx_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ut/5utx ftp://data.pdbj.org/pub/pdb/validation_reports/ut/5utx | HTTPS FTP |
-Related structure data
Related structure data | 1cl0S 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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-Components
#1: Protein | Mass: 34382.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus CMCP6 (bacteria) / Gene: VV1455 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q7MLH2, thioredoxin-disulfide reductase #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE PROTEIN SEQUENCE MATCHES TO GENBANK 27366093. | |
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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: 2.39 Å3/Da / Density % sol: 48.64 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 20% PEG1000, 100 mM potassium/sodium phosphate, 200 mM sodium chloride |
-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 X 6M / Detector: PIXEL / Date: Nov 30, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.45→50 Å / Num. obs: 24257 / % possible obs: 98.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 34.06 Å2 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.027 / Rrim(I) all: 0.071 / Χ2: 0.933 / Net I/σ(I): 9.7 / Num. measured all: 160021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1CL0 Resolution: 2.46→47.83 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.93
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 148.73 Å2 / Biso mean: 50.8994 Å2 / Biso min: 5.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.46→47.83 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Origin x: 78.7074 Å / Origin y: 10.735 Å / Origin z: 4.6334 Å
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Refinement TLS group |
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