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Yorodumi- PDB-1me9: Inosine Monophosphate Dehydrogenase (IMPDH) From Tritrichomonas F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1me9 | ||||||
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Title | Inosine Monophosphate Dehydrogenase (IMPDH) From Tritrichomonas Foetus with IMP 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: 2.2 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1me9.cif.gz | 83.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1me9.ent.gz | 65.4 KB | Display | PDB format |
PDBx/mmJSON format | 1me9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1me9_validation.pdf.gz | 752.3 KB | Display | wwPDB validaton report |
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Full document | 1me9_full_validation.pdf.gz | 757.2 KB | Display | |
Data in XML | 1me9_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 1me9_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/1me9 ftp://data.pdbj.org/pub/pdb/validation_reports/me/1me9 | HTTPS FTP |
-Related structure data
Related structure data | 1mehC 1meiC 1mewC 1ak5S S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 55556.012 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 |
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#2: Chemical | ChemComp-K / |
#3: Chemical | ChemComp-IMP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.44 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 11, 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: 2.2→20 Å / Num. all: 32543 / Num. obs: 32513 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 2.2→2.24 Å / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 2.13 / Num. unique all: 1585 / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 32418 / Num. measured all: 996397 |
Reflection shell | *PLUS % possible obs: 99.8 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1AK5 Resolution: 2.2→19.77 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3506738.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.2427 Å2 / ksol: 0.364722 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 50 Å / Rfactor Rfree: 0.271 / Rfactor Rwork: 0.245 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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