+Open data
-Basic information
Entry | Database: PDB / ID: 2csl | ||||||
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Title | Crystal structure of TTHA0137 from Thermus Thermophilus HB8 | ||||||
Components | protein translation initiation inhibitor | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / 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: 2.5 Å | ||||||
Authors | Wang, H. / Murayama, K. / Terada, T. / Chen, L. / Jin, Z. / Chrzas, J. / Liu, Z.J. / Wang, B.C. / Shirouzu, M. / Kuramitsu, S. ...Wang, H. / Murayama, K. / Terada, T. / Chen, L. / Jin, Z. / Chrzas, J. / Liu, Z.J. / Wang, B.C. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of TTHA0137 from Thermus Thermophilus HB8 Authors: Wang, H. / Murayama, K. / Terada, T. / Chen, L. / Jin, Z. / Chrzas, J. / Liu, Z.J. / Wang, B.C. / Shirouzu, 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 | 2csl.cif.gz | 142.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2csl.ent.gz | 121.3 KB | Display | PDB format |
PDBx/mmJSON format | 2csl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2csl_validation.pdf.gz | 465.7 KB | Display | wwPDB validaton report |
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Full document | 2csl_full_validation.pdf.gz | 484.1 KB | Display | |
Data in XML | 2csl_validation.xml.gz | 30.2 KB | Display | |
Data in CIF | 2csl_validation.cif.gz | 41.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/2csl ftp://data.pdbj.org/pub/pdb/validation_reports/cs/2csl | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13297.769 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SM06 #2: 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: 4.4 Å3/Da / Density % sol: 72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Ammonium Sulfate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9792 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 23, 2005 |
Radiation | Monochromator: SINGLE WAVELENGTH / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 49920 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 52.6 Å2 / Rsym value: 0.076 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 4881 / Rsym value: 0.339 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→45.67 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 131854.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.8723 Å2 / ksol: 0.3348 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 49.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→45.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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