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Yorodumi- PDB-2z06: Crystal structure of uncharacterized conserved protein from Therm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z06 | ||||||
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Title | Crystal structure of uncharacterized conserved protein from Thermus thermophilus | ||||||
Components | Putative uncharacterized protein TTHA0625 | ||||||
Keywords | METAL BINDING PROTEIN / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Kanagawa, M. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of uncharacterized conserved protein from Thermus thermophilus Authors: Kanagawa, M. / Kuramitsu, S. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z06.cif.gz | 208.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z06.ent.gz | 167.8 KB | Display | PDB format |
PDBx/mmJSON format | 2z06.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z06_validation.pdf.gz | 458.3 KB | Display | wwPDB validaton report |
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Full document | 2z06_full_validation.pdf.gz | 488.8 KB | Display | |
Data in XML | 2z06_validation.xml.gz | 43.9 KB | Display | |
Data in CIF | 2z06_validation.cif.gz | 61 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/2z06 ftp://data.pdbj.org/pub/pdb/validation_reports/z0/2z06 | HTTPS FTP |
-Related structure data
Related structure data | 2cv9S 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: 28023.943 Da / Num. of mol.: 4 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) / References: UniProt: Q5SKL8 #2: Chemical | ChemComp-CO / #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: 2.19 Å3/Da / Density % sol: 43.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.2 Details: 0.1M Sodium Acetate, 1.3M Ammonium H2 Phosphate, 0.1M Lithium Sulfate, 0.01M Cobalt Chloride, pH 5.2, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 2, 2006 |
Radiation | Monochromator: Fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 50914 / % possible obs: 97.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.075 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.419 / % possible all: 83.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CV9 Resolution: 2.2→36.2 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 97897.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.9 Å2 / ksol: 0.374449 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→36.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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