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Yorodumi- PDB-1ve4: ATP-Phosphoribosyltransferase(hisG) from Thermus thermophilus HB8 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ve4 | ||||||
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Title | ATP-Phosphoribosyltransferase(hisG) from Thermus thermophilus HB8 | ||||||
Components | ATP phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / L-histidine biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.2 Å | ||||||
Authors | Omi, R. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of ATP-phosphoribosyltransferase(HisG) Authors: Omi, R. / Goto, M. / Miyahara, I. / Hirotsu, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ve4.cif.gz | 55.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ve4.ent.gz | 39.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ve4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/1ve4 ftp://data.pdbj.org/pub/pdb/validation_reports/ve/1ve4 | 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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-Components
#1: Protein | Mass: 22414.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62381, ATP phosphoribosyltransferase |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.78 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 5, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→28.04 Å / Num. all: 61195 / Num. obs: 61195 / % possible obs: 98.7 % / Biso Wilson estimate: 10.6 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.2→28.04 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1041497.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: Resolution-Dependent weighting scheme, Bulk solvent model used
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.4622 Å2 / ksol: 0.385921 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.2→28.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.28 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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