[English] 日本語
Yorodumi- PDB-1mew: Inosine Monophosphate Dehydrogenase (IMPDH) From Tritrichomonas F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mew | ||||||
---|---|---|---|---|---|---|---|
Title | Inosine Monophosphate Dehydrogenase (IMPDH) From Tritrichomonas Foetus with XMP and NAD 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. / Luecke, H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Crystal Structures of Tritrichomonas foetus Inosine Monophosphate Dehydrogenase in Complex with Substrate, Cofactor and Analogs: A Structural Basis for the Random-in Ordered-out Kinetic Mechanism Authors: Prosise, G.L. / Luecke, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1mew.cif.gz | 83.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1mew.ent.gz | 65.4 KB | Display | PDB format |
PDBx/mmJSON format | 1mew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mew_validation.pdf.gz | 1016.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1mew_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1mew_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 1mew_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/1mew ftp://data.pdbj.org/pub/pdb/validation_reports/me/1mew | HTTPS FTP |
-Related structure data
Related structure data | 1me9C 1mehC 1meiC 1ak5S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#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 |
---|---|
#2: Chemical | ChemComp-K / |
#3: Chemical | ChemComp-XMP / |
#4: Chemical | ChemComp-NAD / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.94 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. all: 34423 / Num. obs: 33857 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.15→2.19 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1604 / % possible all: 95.9 |
Reflection | *PLUS Num. measured all: 734853 / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS Lowest resolution: 2.28 Å / % possible obs: 95.9 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2.22 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 1AK5 Resolution: 2.15→29.61 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3426655.95 / 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: 41.9441 Å2 / ksol: 0.384288 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.1 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→29.61 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.15→2.28 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rwork: 0.223 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|