[English] 日本語
Yorodumi- PDB-1me7: Inosine Monophosphate Dehydrogenase (IMPDH) From Tritrichomonas F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1me7 | ||||||
---|---|---|---|---|---|---|---|
Title | Inosine Monophosphate Dehydrogenase (IMPDH) From Tritrichomonas Foetus with RVP and MOA bound | ||||||
Components | INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / alpha beta barrel | ||||||
Function / homology | Function and homology information IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / nucleotide binding / protein-containing complex / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Tritrichomonas foetus (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å | ||||||
Authors | Prosise, G.L. / Wu, J. / Luecke, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Crystal Structure of Tritrichomonas foetus Inosine Monophosphate Dehydrogenase in Complex with the Inhibitor Ribavirin Monophosphate Reveals a Catalysis-dependent Ion-binding Site Authors: Prosise, G.L. / Wu, J. / Luecke, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1me7.cif.gz | 85.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1me7.ent.gz | 67.7 KB | Display | PDB format |
PDBx/mmJSON format | 1me7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1me7_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1me7_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1me7_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 1me7_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/1me7 ftp://data.pdbj.org/pub/pdb/validation_reports/me/1me7 | HTTPS FTP |
-Related structure data
Related structure data | 1me8C 1ak5S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 55540.012 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tritrichomonas foetus (eukaryote) / Gene: IMPDH / Plasmid: pBACE / Production host: Escherichia coli (E. coli) / Strain (production host): H712 / References: UniProt: P50097, IMP dehydrogenase |
---|
-Non-polymers , 5 types, 124 molecules
#2: Chemical | ChemComp-NA / |
---|---|
#3: Chemical | ChemComp-K / |
#4: Chemical | ChemComp-RVP / |
#5: Chemical | ChemComp-MOA / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.02 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: sodium malonate, Tris, 2-mercaptoethanol, EDTA, glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 12, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. all: 35240 / Num. obs: 33143 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 33.1 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 2.05 |
Reflection shell | Resolution: 2.15→2.19 Å / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.05 / Num. unique all: 1354 / % possible all: 79.5 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 35250 / Num. measured all: 620781 |
Reflection shell | *PLUS Lowest resolution: 2.28 Å / % possible obs: 79.5 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 1AK5 Resolution: 2.15→49.04 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3210639.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.5379 Å2 / ksol: 0.361162 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.7 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→49.04 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.15→2.28 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / Rfactor Rfree: 0.265 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|