+Open data
-Basic information
Entry | Database: PDB / ID: 1g9t | ||||||
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Title | CRYSTAL STRUCTURE OF E.COLI HPRT-GMP COMPLEX | ||||||
Components | HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASEHypoxanthine-guanine phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / phosphoribosyltransferases / purine salvage / protein chemistry / enzymology | ||||||
Function / homology | Function and homology information guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / purine ribonucleoside salvage / guanosine tetraphosphate binding / protein homotetramerization ...guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / purine ribonucleoside salvage / guanosine tetraphosphate binding / protein homotetramerization / magnesium ion binding / protein-containing complex / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Guddat, L.W. / Vos, S. / Martin, J.L. / keough, D.T. / de Jersey, J. | ||||||
Citation | Journal: Protein Sci. / Year: 2002 Title: Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase. Authors: Guddat, L.W. / Vos, S. / Martin, J.L. / Keough, D.T. / de Jersey, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g9t.cif.gz | 81.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g9t.ent.gz | 60.8 KB | Display | PDB format |
PDBx/mmJSON format | 1g9t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/1g9t ftp://data.pdbj.org/pub/pdb/validation_reports/g9/1g9t | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20657.887 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: HPT / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): SPHI606 References: UniProt: P0A9M2, hypoxanthine phosphoribosyltransferase #2: Chemical | ChemComp-5GP / | #3: Chemical | ChemComp-N / | #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: 4.14 Å3/Da / Density % sol: 70.26 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Hepes, sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.4 | |||||||||||||||||||||||||||||||||||||||||||||||||
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: APS / Beamline: 14-BM-D / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 1 / Detector: CCD / Date: Dec 20, 1999 / Details: mirrors |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 15697 / Num. obs: 45289 / % possible obs: 88.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1388 / % possible all: 89.8 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 15697 / Num. measured all: 45289 / Rmerge(I) obs: 0.072 |
Reflection shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 89.8 % / Rmerge(I) obs: 0.294 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: T.foetus HPRT Resolution: 2.8→50 Å / Cross valid method: USED THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: simulated annealing refinement
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Displacement parameters | Biso mean: 38.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.9 Å / Rfactor Rfree error: 0.012
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor all: 0.199 / Rfactor Rfree: 0.244 / Rfactor Rwork: 0.199 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.38 | ||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.3338 / Rfactor Rwork: 0.2748 |