+Open data
-Basic information
Entry | Database: PDB / ID: 1otx | ||||||
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Title | Purine Nucleoside Phosphorylase M64V mutant | ||||||
Components | Purine nucleoside phosphorylase | ||||||
Keywords | TRANSFERASE / empty / PNP | ||||||
Function / homology | Function and homology information purine nucleoside interconversion / guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine nucleoside catabolic process / purine-nucleoside phosphorylase activity / DNA damage response / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Ealick, S.E. / Bennett, E.M. / Anand, R. / Secrist, J.A. / Parker, W.B. / Hassan, A.E. / Allan, P.W. / McPherson, D.T. / Sorscher, E.J. | ||||||
Citation | Journal: Chem.Biol. / Year: 2003 Title: Designer gene therapy using an Escherichia coli purine nucleoside phosphorylase/prodrug system. Authors: Bennett, E.M. / Anand, R. / Allan, P.W. / Hassan, A.E. / Hong, J.S. / Levasseur, D.N. / McPherson, D.T. / Parker, W.B. / Secrist, J.A. / Sorscher, E.J. / Townes, T.M. / Waud, W.R. / Ealick, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1otx.cif.gz | 145.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1otx.ent.gz | 116.5 KB | Display | PDB format |
PDBx/mmJSON format | 1otx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1otx_validation.pdf.gz | 460.6 KB | Display | wwPDB validaton report |
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Full document | 1otx_full_validation.pdf.gz | 479.2 KB | Display | |
Data in XML | 1otx_validation.xml.gz | 30.4 KB | Display | |
Data in CIF | 1otx_validation.cif.gz | 41.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/1otx ftp://data.pdbj.org/pub/pdb/validation_reports/ot/1otx | HTTPS FTP |
-Related structure data
Related structure data | 1otyC 1ou4C 1oumC 1ov6C 1ovgC 1ecpS 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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-Components
#1: Protein | Mass: 25818.684 Da / Num. of mol.: 3 / Mutation: M64V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) References: UniProt: P0ABP8, purine-nucleoside phosphorylase #2: Chemical | #3: 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: 3.18 Å3/Da / Density % sol: 61 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 50mM sodium citrate, 30%ammonium sulfate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.948 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 24, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.948 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→25 Å / Num. all: 28800 / Num. obs: 28781 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.3 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 6.2 / Num. unique all: 2880 / Rsym value: 0.1 / % possible all: 100 |
Reflection | *PLUS Rmerge(I) obs: 0.1 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 3.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ECP Resolution: 2.7→24.36 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.554 Å2 / ksol: 0.403784 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→24.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.251 / Rfactor Rwork: 0.206 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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