+Open data
-Basic information
Entry | Database: PDB / ID: 1s3f | ||||||
---|---|---|---|---|---|---|---|
Title | Purine 2'-deoxyribosyltransferase + selenoinosine | ||||||
Components | purine trans deoxyribosylase | ||||||
Keywords | TRANSFERASE / selenoinosine complex | ||||||
Function / homology | Function and homology information nucleoside deoxyribosyltransferase / nucleoside deoxyribosyltransferase activity Similarity search - Function | ||||||
Biological species | Lactobacillus helveticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Anand, R. / Kaminski, P.A. / Ealick, S.E. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Structures of purine 2'-deoxyribosyltransferase, substrate complexes, and the ribosylated enzyme intermediate at 2.0 A resolution. Authors: Anand, R. / Kaminski, P.A. / Ealick, S.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1s3f.cif.gz | 102.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1s3f.ent.gz | 79.9 KB | Display | PDB format |
PDBx/mmJSON format | 1s3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/1s3f ftp://data.pdbj.org/pub/pdb/validation_reports/s3/1s3f | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18733.189 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus helveticus (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: Q8RLY5, nucleoside deoxyribosyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.49 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 2.0 M ammonium sulfate, 100mM tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 170 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 35106 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.256 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.94 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 582369.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.8318 Å2 / ksol: 0.373143 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.5 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→19.94 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
|