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Yorodumi- PDB-1rtw: X-ray Structure of PF1337, a TenA Homologue from Pyrococcus furio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rtw | ||||||
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Title | X-ray Structure of PF1337, a TenA Homologue from Pyrococcus furiosus. Northeast Structural Genomics Research Consortium (Nesg) Target PFR34 | ||||||
Components | transcriptional activator, putative | ||||||
Keywords | structural genomics / unknown function / pf1337 / tena / thiamin / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information small molecule metabolic process / sulfur compound metabolic process / cytosol Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.35 Å | ||||||
Authors | Benach, J. / Edstrom, W.C. / Lee, I. / Rong, X. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: The 2.35 A structure of the TenA homolog from Pyrococcus furiosus supports an enzymatic function in thiamine metabolism. Authors: Benach, J. / Edstrom, W.C. / Lee, I. / Das, K. / Cooper, B. / Xiao, R. / Liu, J. / Rost, B. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. | ||||||
History |
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Remark 600 | ligand THE NATURE OF THE LIGAND IS TENTATIVE. THE LIGAND MP5 IS IS CLEARLY VISIBLE ONLY IN MONOMER ...ligand THE NATURE OF THE LIGAND IS TENTATIVE. THE LIGAND MP5 IS IS CLEARLY VISIBLE ONLY IN MONOMER A. IN THE OTHER MONOMERS, ONLY THE PHOSPHATE PART OF THE LIGAND HAS BEEN MODELLED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rtw.cif.gz | 186.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rtw.ent.gz | 152.2 KB | Display | PDB format |
PDBx/mmJSON format | 1rtw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rtw_validation.pdf.gz | 492.7 KB | Display | wwPDB validaton report |
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Full document | 1rtw_full_validation.pdf.gz | 514.2 KB | Display | |
Data in XML | 1rtw_validation.xml.gz | 39.6 KB | Display | |
Data in CIF | 1rtw_validation.cif.gz | 51.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/1rtw ftp://data.pdbj.org/pub/pdb/validation_reports/rt/1rtw | HTTPS FTP |
-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: 26761.631 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Plasmid: pET21d / Production host: Escherichia coli (E. coli) Strain (production host): BL21(DE3) containing rare-tRNA expression plasmid pMGK References: UniProt: Q8U189 #2: Chemical | ChemComp-MP5 / ( | #3: Chemical | #4: Water | ChemComp-HOH / | Has protein modification | Y | |
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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: 2.4 Å3/Da / Density % sol: 48.67 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG400, 200mM CaCl2, 50mM cacodylic acid, 1mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / pH: 8 / 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: NSLS / Beamline: X12C / Wavelength: 0.979, 0.9794, 0.95 | ||||||||||||
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Sep 12, 2003 | ||||||||||||
Radiation | Monochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.35→100 Å / Num. obs: 40075 / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 18.7 | ||||||||||||
Reflection shell | Resolution: 2.35→2.38 Å / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 3.7 | ||||||||||||
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 73637 / % possible obs: 93.5 % / Redundancy: 3.3 % / Num. measured all: 239958 / Rmerge(I) obs: 0.07 | ||||||||||||
Reflection shell | *PLUS Lowest resolution: 2.43 Å / % possible obs: 89.7 % / Redundancy: 3.3 % / Num. unique obs: 6861 / Num. measured obs: 22349 / Rmerge(I) obs: 0.33 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.35→20 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.35→20 Å
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree: 0.28 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.35 Å / Lowest resolution: 2.43 Å / Rfactor Rfree: 0.31 / Rfactor Rwork: 0.27 |