[English] 日本語
Yorodumi- PDB-3acd: Crystal structure of hypoxanthine-guanine phosphoribosyltransfera... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3acd | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of hypoxanthine-guanine phosphoribosyltransferase with IMP from Thermus thermophilus HB8 | |||||||||
Components | Hypoxanthine-guanine phosphoribosyltransferase | |||||||||
Keywords | TRANSFERASE / Rossmann fold / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | |||||||||
Function / homology | Function and homology information hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / purine ribonucleoside salvage / nucleotide binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Thermus thermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | |||||||||
Authors | Kanagawa, M. / Baba, S. / Hirotsu, K. / Kuramitsu, S. / Yokoyama, S. / Kawai, G. / Sampei, G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Structures of hypoxanthine-guanine phosphoribosyltransferase (TTHA0220) from Thermus thermophilus HB8. Authors: Kanagawa, M. / Baba, S. / Ebihara, A. / Shinkai, A. / Hirotsu, K. / Mega, R. / Kim, K. / Kuramitsu, S. / Sampei, G. / Kawai, G. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3acd.cif.gz | 52 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3acd.ent.gz | 35.8 KB | Display | PDB format |
PDBx/mmJSON format | 3acd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/3acd ftp://data.pdbj.org/pub/pdb/validation_reports/ac/3acd | HTTPS FTP |
---|
-Related structure data
Related structure data | 3acbSC 3accC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20193.264 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0220 / Plasmid: pET-11A / Production host: Escherichia coli (E. coli) References: UniProt: Q5SLS3, hypoxanthine phosphoribosyltransferase | ||
---|---|---|---|
#2: Chemical | ChemComp-IMP / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.12 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 15% Glycerol, 29% Dioxane, 0.01M IMP, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 23, 2007 |
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: 1.89→50 Å / Num. obs: 17152 / % possible obs: 99.9 % / Redundancy: 10.7 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.045 |
Reflection shell | Resolution: 1.89→1.96 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.141 / Num. unique all: 1583 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ACB Resolution: 1.89→38.27 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 192076.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.2263 Å2 / ksol: 0.414341 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.2 Å2
| ||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→38.27 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 1.89→2.01 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
| ||||||||||||||||||||||||
Xplor file |
|