[English] 日本語
Yorodumi- PDB-1q1g: Crystal structure of Plasmodium falciparum PNP with 5'-methylthio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q1g | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Plasmodium falciparum PNP with 5'-methylthio-immucillin-H | ||||||
Components | Uridine phosphorylase putative | ||||||
Keywords | TRANSFERASE / TRANSITION STATE COMPLEX | ||||||
Function / homology | Function and homology information Pyrimidine salvage / Pyrimidine catabolism / S-methyl-5'-thioinosine phosphorylase / purine nucleotide catabolic process / S-methyl-5-thioadenosine phosphorylase activity / inosine catabolic process / uridine catabolic process / uridine phosphorylase activity / guanosine phosphorylase activity / purine-nucleoside phosphorylase ...Pyrimidine salvage / Pyrimidine catabolism / S-methyl-5'-thioinosine phosphorylase / purine nucleotide catabolic process / S-methyl-5-thioadenosine phosphorylase activity / inosine catabolic process / uridine catabolic process / uridine phosphorylase activity / guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine ribonucleoside salvage / cytosol Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.02 Å | ||||||
Authors | Shi, W. / Ting, L.M. / Kicska, G.A. / Lewandowicz, A. / Tyler, P.C. / Evans, G.B. / Furneaux, R.H. / Kim, K. / Almo, S.C. / Schramm, V.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Plasmodium falciparum Purine Nucleoside Phosphorylase: CRYSTAL STRUCTURES, IMMUCILLIN INHIBITORS, AND DUAL CATALYTIC FUNCTION. Authors: Shi, W. / Ting, L.M. / Kicska, G.A. / Lewandowicz, A. / Tyler, P.C. / Evans, G.B. / Furneaux, R.H. / Kim, K. / Almo, S.C. / Schramm, V.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1q1g.cif.gz | 301.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1q1g.ent.gz | 242.8 KB | Display | PDB format |
PDBx/mmJSON format | 1q1g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/1q1g ftp://data.pdbj.org/pub/pdb/validation_reports/q1/1q1g | HTTPS FTP |
---|
-Related structure data
Related structure data | 1nw4SC 1rr6C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is the hexamer in the asymmetric unit. |
-Components
#1: Protein | Mass: 30502.039 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: 3D7 / Plasmid: PTRCHIS2-TOPO / Production host: Escherichia coli (E. coli) References: UniProt: Q8I3X4, purine-nucleoside phosphorylase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-MTI / #4: Chemical | ChemComp-IPA / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.46 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: AMMONIUM SULFATE, ISOPROPANOL, , pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 10, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→30 Å / Num. all: 116751 / Num. obs: 116751 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 15.5 Å2 / Rsym value: 0.047 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.02→2.09 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 11529 / Rsym value: 0.171 / % possible all: 93.8 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1NW4 Resolution: 2.02→30 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Displacement parameters | Biso mean: 29.3 Å2
| ||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→30 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
LS refinement shell | Resolution: 2.02→2.15 Å / Rfactor Rfree error: 0.007
| ||||||||||||||||||||
Refine LS restraints | *PLUS
|