+Open data
-Basic information
Entry | Database: PDB / ID: 1g2p | ||||||
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Title | CRYSTAL STRUCTURE OF ADENINE PHOSPHORIBOSYLTRANSFERASE | ||||||
Components | ADENINE PHOSPHORIBOSYLTRANSFERASE 1 | ||||||
Keywords | TRANSFERASE / dimer / catalytic loop | ||||||
Function / homology | Function and homology information Purine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase activity / adenine phosphoribosyltransferase / AMP salvage / purine ribonucleoside salvage / AMP binding / Neutrophil degranulation / metal ion binding ...Purine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase activity / adenine phosphoribosyltransferase / AMP salvage / purine ribonucleoside salvage / AMP binding / Neutrophil degranulation / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Shi, W. / Tanaka, K.S.E. / Almo, S.C. / Schramm, V.L. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Structural analysis of adenine phosphoribosyltransferase from Saccharomyces cerevisiae. Authors: Shi, W. / Tanaka, K.S. / Crother, T.R. / Taylor, M.W. / Almo, S.C. / Schramm, V.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g2p.cif.gz | 47.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g2p.ent.gz | 33.7 KB | Display | PDB format |
PDBx/mmJSON format | 1g2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/1g2p ftp://data.pdbj.org/pub/pdb/validation_reports/g2/1g2p | HTTPS FTP |
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-Related structure data
Related structure data | 1g2qC 1qb8S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The second part of the biological assemble is generated by the two fold screw axis, -x, -y+1/2, z |
-Components
#1: Protein | Mass: 20616.814 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: PQE / Production host: Escherichia coli (E. coli) References: UniProt: P49435, adenine phosphoribosyltransferase | ||
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#2: Chemical | #3: 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: 3.19 Å3/Da / Density % sol: 61 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: lithium sulfate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||
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: X9B / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 11, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20 Å / Num. all: 26348 / Num. obs: 26348 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 15.9 Å2 / Rsym value: 0.041 / Net I/σ(I): 29.6 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 1134 / Rsym value: 0.24 / % possible all: 82.8 |
Reflection | *PLUS Num. measured all: 103449 / Rmerge(I) obs: 0.041 |
Reflection shell | *PLUS % possible obs: 82.8 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1QB8 Resolution: 1.75→20 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1.4 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: Flat model / Bsol: 49.4464 Å2 / ksol: 0.370397 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 9.8 % / Rfactor all: 0.21 / Rfactor obs: 0.208 / Rfactor Rfree: 0.23 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28.6 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.329 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.3 |