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Yorodumi- PDB-3or5: Crystal structure of thiol:disulfide interchange protein, thiored... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3or5 | ||||||
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Title | Crystal structure of thiol:disulfide interchange protein, thioredoxin family protein from Chlorobium tepidum TLS | ||||||
Components | Thiol:disulfide interchange protein, thioredoxin family protein | ||||||
Keywords | OXIDOREDUCTASE / PSI-II / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information cytochrome complex assembly / cell redox homeostasis / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Chlorobaculum tepidum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.66 Å | ||||||
Authors | Bagaria, A. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of thiol:disulfide interchange protein, thioredoxin family protein from Chlorobium tepidum TLS Authors: Bagaria, A. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3or5.cif.gz | 39.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3or5.ent.gz | 30.1 KB | Display | PDB format |
PDBx/mmJSON format | 3or5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/3or5 ftp://data.pdbj.org/pub/pdb/validation_reports/or/3or5 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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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: 18037.754 Da / Num. of mol.: 1 / Fragment: sequence database residues 25-178 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlorobaculum tepidum (bacteria) / Strain: TLS / Gene: CT2233 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KAD0 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M BIS-TRIS pH 6.5, 3.0 M Sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 19, 2010 / Details: Mirrors |
Radiation | Monochromator: Si(111)channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→38 Å / Num. all: 18281 / Num. obs: 18223 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 27.9 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.66→1.7 Å / Redundancy: 28.1 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2 / Num. unique all: 1254 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.66→37.99 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.53 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.089 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.382 Å2
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Refinement step | Cycle: LAST / Resolution: 1.66→37.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.662→1.705 Å / Total num. of bins used: 20
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