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Yorodumi- PDB-1i80: CRYSTAL STRUCTURE OF M. TUBERCULOSIS PNP IN COMPLEX WITH IMINORIB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i80 | ||||||
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Title | CRYSTAL STRUCTURE OF M. TUBERCULOSIS PNP IN COMPLEX WITH IMINORIBITOL, 9-DEAZAHYPOXANTHINE AND PHOSPHATE ION | ||||||
Components | PURINE NUCLEOSIDE PHOSPHORYLASE | ||||||
Keywords | TRANSFERASE / TRIMER / TRANSITION-STATE COMPLEX | ||||||
Function / homology | Function and homology information deoxyguanosine catabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Shi, W. / Basso, L.A. / Tyler, P.C. / Furneaux, R.H. / Blanchard, J.S. / Almo, S.C. / Schramm, V.L. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Structures of purine nucleoside phosphorylase from Mycobacterium tuberculosis in complexes with immucillin-H and its pieces. Authors: Shi, W. / Basso, L.A. / Santos, D.S. / Tyler, P.C. / Furneaux, R.H. / Blanchard, J.S. / 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 | 1i80.cif.gz | 157.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i80.ent.gz | 123.8 KB | Display | PDB format |
PDBx/mmJSON format | 1i80.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/1i80 ftp://data.pdbj.org/pub/pdb/validation_reports/i8/1i80 | HTTPS FTP |
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-Related structure data
Related structure data | 1g2oSC 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 biological assembly is the trimer in the asymmetric unit. |
-Components
#1: Protein | Mass: 27599.457 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: PET-23A(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P0A538, UniProt: P9WP01*PLUS, purine-nucleoside phosphorylase #2: Chemical | ChemComp-PO4 / | #3: Chemical | #4: Chemical | ChemComp-IMR / | #5: 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: 2.21 Å3/Da / Density % sol: 44.41 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 4000, MAGNESIUM CHLORIDE, TRIS BUFFER, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 44 % | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | ||||||||||||||||||||||||||||||||||||||||||
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: Oct 20, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 48026 / Num. obs: 48026 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 10.8 Å2 / Rsym value: 0.073 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 4.5 / Rsym value: 0.202 / % possible all: 83.9 |
Reflection | *PLUS Num. measured all: 176063 / Rmerge(I) obs: 0.073 |
Reflection shell | *PLUS % possible obs: 83.9 % / Rmerge(I) obs: 0.206 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G2O Resolution: 2→20 Å / Rfactor Rfree error: 0.004 / 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: 45.91 Å2 / ksol: 0.376 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor all: 0.209 / Rfactor obs: 0.206 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 23.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.255 / % reflection Rfree: 10 % / Rfactor Rwork: 0.203 |