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Yorodumi- PDB-1ukk: Structure of Osmotically Inducible Protein C from Thermus thermophilus -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ukk | ||||||
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Title | Structure of Osmotically Inducible Protein C from Thermus thermophilus | ||||||
Components | Osmotically Inducible Protein C | ||||||
Keywords | OXIDOREDUCTASE / peroxidase / cysteinesulfinic acid / osmotic / inducible / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å | ||||||
Authors | Rehse, P.H. / Kuramitsu, S. / Yokoyama, S. / Miyano, M. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.MOL.BIOL. / Year: 2004 Title: Crystallographic Structure and Biochemical Analysis of the Thermus thermophilus Osmotically Inducible Protein C Authors: Rehse, P.H. / Oshima, N. / Nodaka, Y. / Tahirov, T.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ukk.cif.gz | 71.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ukk.ent.gz | 53.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ukk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uk/1ukk ftp://data.pdbj.org/pub/pdb/validation_reports/uk/1ukk | 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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Details | The biological assembly corresponds to the dimer found in the assymetric unit. |
-Components
#1: Protein | Mass: 15456.159 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P84124 #2: Chemical | ChemComp-TRS / | #3: 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: 1.9 Å3/Da / Density % sol: 34.61 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.4 Details: PEG 4000, Tris-HCl, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97894, 0.97910, 0.97920, 0.97500, 1.000 | ||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 28, 2003 / Details: mirrors | ||||||||||||||||||
Radiation | Monochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→20 Å / Num. all: 30286 / Num. obs: 30286 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.85 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 15 | ||||||||||||||||||
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 1.76 % / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 4.1 / % possible all: 79.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.6→8 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.12 / SU ML: 0.074 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.106 / ESU R Free: 0.112 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.284 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.64 Å / Total num. of bins used: 20 /
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