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Yorodumi- PDB-3iom: Crystal structure of Purine Nucleoside Phosphorylase from Mycobac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3iom | ||||||
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Title | Crystal structure of Purine Nucleoside Phosphorylase from Mycobacterium tuberculosis in complex with 2'-Deoxyguanosine | ||||||
Components | Purine nucleoside phosphorylase | ||||||
Keywords | TRANSFERASE / Purine Nucleoside Phosphorylase / Mycobacterium tuberculosis / 2 -deoxyguanosine / Glycosyltransferase | ||||||
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: 2.14 Å | ||||||
Authors | de Azevedo Jr., W.F. / Basso, L.A. / Santos, D.S. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2010 Title: Crystallographic and docking studies of purine nucleoside phosphorylase from Mycobacterium tuberculosis. Authors: Ducati, R.G. / Basso, L.A. / Santos, D.S. / de Azevedo, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3iom.cif.gz | 111.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iom.ent.gz | 86.5 KB | Display | PDB format |
PDBx/mmJSON format | 3iom.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/3iom ftp://data.pdbj.org/pub/pdb/validation_reports/io/3iom | HTTPS FTP |
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-Related structure data
Related structure data | 1g2oS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | 2 |
-Components
#1: Protein | Mass: 27599.457 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: Mycobacterium tuberculosis Gene: deoD, MT3406, MTV016.06, punA, punA (deoD) (Rv3307) (MT3406) (MTV016.06), Rv3307 Production host: Escherichia coli (E. coli) References: UniProt: P0A538, UniProt: P9WP01*PLUS, purine-nucleoside phosphorylase #2: Chemical | #3: Chemical | #4: 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: 1.91 Å3/Da / Density % sol: 35.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: The protein was cocrystallized with a 1:0.5:1 stoichiometry of 500 mM Na2SO4 (Merck) and 3 mM 2dGuo (Fluka Biochemika), respectively, by hanging-drop vapor diffusion at 18 C. MtPNP protein ...Details: The protein was cocrystallized with a 1:0.5:1 stoichiometry of 500 mM Na2SO4 (Merck) and 3 mM 2dGuo (Fluka Biochemika), respectively, by hanging-drop vapor diffusion at 18 C. MtPNP protein (1 L of 25 mg mL-1 in 50 mM tris(hydroxymethyl)aminomethane (Tris) pH 7.6) had been previously mixed with an equal volume of the reservoir solution containing 100 mM Tris pH 8.0, 25% poly(ethylene glycol) (PEG) 3350, and 25 mM MgCl2 and hanging drops (3.5 L) were equilibrated against 400 L of the reservoir solution. , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.428 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 2, 2009 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.428 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→28.69 Å / Num. all: 22411 / Num. obs: 22163 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Biso Wilson estimate: 21.642 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 3.5 / Num. unique all: 625 / Rsym value: 0.138 / % possible all: 81.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1G2O Resolution: 2.14→28.34 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.87 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.352 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.181 Å2
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Refinement step | Cycle: LAST / Resolution: 2.14→28.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.143→2.198 Å / Total num. of bins used: 20
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