+
Open data
-
Basic information
Entry | Database: PDB / ID: 1g2p | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF ADENINE PHOSPHORIBOSYLTRANSFERASE | ||||||
![]() | ADENINE PHOSPHORIBOSYLTRANSFERASE 1 | ||||||
![]() | TRANSFERASE / dimer / catalytic loop | ||||||
Function / homology | ![]() Purine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / AMP salvage / purine ribonucleoside salvage / AMP binding / Neutrophil degranulation / nucleus ...Purine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / AMP salvage / purine ribonucleoside salvage / AMP binding / Neutrophil degranulation / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shi, W. / Tanaka, K.S.E. / Almo, S.C. / Schramm, V.L. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 47.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 33.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 378.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 379.9 KB | Display | |
Data in XML | ![]() | 5.2 KB | Display | |
Data in CIF | ![]() | 7.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1g2qC ![]() 1qb8S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
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.) ![]() ![]() Plasmid: PQE / Production host: ![]() ![]() References: UniProt: P49435, adenine phosphoribosyltransferase | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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 |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: Flat model / Bsol: 49.4464 Å2 / ksol: 0.370397 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.6 Å2
| ||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→20 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.329 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.3 |