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Yorodumi- PDB-1n3i: Crystal Structure of Mycobacterium tuberculosis PNP with transiti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n3i | |||||||||
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Title | Crystal Structure of Mycobacterium tuberculosis PNP with transition state analog DADMe-ImmH | |||||||||
Components | Purine Nucleoside Phosphorylase | |||||||||
Keywords | TRANSFERASE / transition state complex / trimer / PNP | |||||||||
Function / homology | Function and homology information deoxyguanosine catabolic process / beta-alanine metabolic process / pantoate-beta-alanine ligase (AMP-forming) / pantoate-beta-alanine ligase activity / pantothenate biosynthetic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / manganese ion binding / magnesium ion binding / ATP binding ...deoxyguanosine catabolic process / beta-alanine metabolic process / pantoate-beta-alanine ligase (AMP-forming) / pantoate-beta-alanine ligase activity / pantothenate biosynthetic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / manganese ion binding / magnesium ion binding / ATP binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å | |||||||||
Authors | Lewandowicz, A. / Shi, W. / Evans, G.B. / Tyler, P.C. / Furneaux, R.H. / Basso, L.A. / Santos, D.S. / Almo, S.C. / Schramm, V.L. | |||||||||
Citation | Journal: BIOCHEMISTRY / Year: 2003 Title: Over-The-Barrier Transition State Analogues Provide New Chemistries for Inhibitor Design: The Case of Purine Nucleoside Phosphorylase Authors: Lewandowicz, A. / Shi, W. / Evans, G.B. / Tyler, P.C. / Furneaux, R.H. / Basso, L.A. / Santos, D.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 | 1n3i.cif.gz | 158.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n3i.ent.gz | 125.7 KB | Display | PDB format |
PDBx/mmJSON format | 1n3i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/1n3i ftp://data.pdbj.org/pub/pdb/validation_reports/n3/1n3i | 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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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: P9WIL5*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: 2.37 Å3/Da / Density % sol: 48.15 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG4000, Magnesium Chloride, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 10, 2002 |
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 62570 / Num. obs: 59925 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 12.9 Å2 / Rsym value: 0.036 / Net I/σ(I): 45.9 |
Reflection shell | Resolution: 1.9→1.97 Å / Mean I/σ(I) obs: 10.3 / Rsym value: 0.105 / % possible all: 76.9 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 321763 / Rmerge(I) obs: 0.036 |
Reflection shell | *PLUS % possible obs: 76.9 % / Rmerge(I) obs: 0.105 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1G2O Resolution: 1.9→20 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 18 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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