+Open data
-Basic information
Entry | Database: PDB / ID: 1uf9 | ||||||
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Title | Crystal structure of TT1252 from Thermus thermophilus | ||||||
Components | TT1252 protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / p-loop / nucleotide binding domain / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information dephospho-CoA kinase / dephospho-CoA kinase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Seto, A. / Murayama, K. / Toyama, M. / Ebihara, A. / Nakagawa, N. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: PROTEINS / Year: 2005 Title: ATP-induced structural change of dephosphocoenzyme A kinase from Thermus thermophilus HB8 Authors: Seto, A. / Murayama, K. / Toyama, M. / Ebihara, A. / Nakagawa, N. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uf9.cif.gz | 124.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uf9.ent.gz | 98.9 KB | Display | PDB format |
PDBx/mmJSON format | 1uf9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uf9_validation.pdf.gz | 478.6 KB | Display | wwPDB validaton report |
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Full document | 1uf9_full_validation.pdf.gz | 501.3 KB | Display | |
Data in XML | 1uf9_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 1uf9_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/1uf9 ftp://data.pdbj.org/pub/pdb/validation_reports/uf/1uf9 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 22859.820 Da / Num. of mol.: 3 / Fragment: nucleotide binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q56416 #2: Chemical | ChemComp-PO4 / | #3: Chemical | ChemComp-ATP / | #4: 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: 2.88 Å3/Da / Density % sol: 57.31 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 0.72M sodium citrate, 90mM imidazole, 10% PEG3000, 10mM CHES, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9793 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 26, 2002 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 18914 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 34.7 Å2 / Rsym value: 0.093 |
Reflection shell | Resolution: 2.8→2.9 Å / Mean I/σ(I) obs: 7.5 / Rsym value: 0.298 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 159215 / Rmerge(I) obs: 0.093 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.298 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→19.65 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1777090.52 / 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: 27.9993 Å2 / ksol: 0.306747 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→19.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.2997 / Rfactor Rwork: 0.2222 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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