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Yorodumi- PDB-1pvn: The crystal structure of the complex between IMP dehydrogenase ca... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pvn | |||||||||
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Title | The crystal structure of the complex between IMP dehydrogenase catalytic domain and a transition state analogue MZP | |||||||||
Components | Inosine-5'-monophosphate dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / Transition state analogue / IMP dehydrogenase / Mizoribine 5'-monophosphate / distal flap / general base / drug selectivity | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Gan, L. / Seyedsayamdost, M. / Shuto, S. / Matsuda, A. / Petsko, G.A. / Hedstrom, L. | |||||||||
Citation | Journal: Biochemistry / Year: 2003 Title: The Immunosuppressive Agent Mizoribine Monophosphate Forms a Transition State Analogue Complex with Inosine Monophosphate Dehydrogenase Authors: Gan, L. / Seyedsayamdost, M. / Shuto, S. / Matsuda, A. / Petsko, G.A. / Hedstrom, L. | |||||||||
History |
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Remark 999 | SEQUENCE IMP dehydrogenase in this structure is a subdomain-deletion mutant. It only contains the ...SEQUENCE IMP dehydrogenase in this structure is a subdomain-deletion mutant. It only contains the catalytic domain with residues 2 to 100 and 227 to 503. Residues 100, 227-230 and 495-503 are disordered in the structure |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pvn.cif.gz | 310.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pvn.ent.gz | 247.6 KB | Display | PDB format |
PDBx/mmJSON format | 1pvn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/1pvn ftp://data.pdbj.org/pub/pdb/validation_reports/pv/1pvn | HTTPS FTP |
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-Related structure data
Related structure data | 1lrtS 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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-Components
#1: Protein | Mass: 41212.914 Da / Num. of mol.: 4 / Fragment: Catalytic core domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tritrichomonas foetus (eukaryote) / Gene: IMPDH / Plasmid: pKK233-3 / Production host: Escherichia coli (E. coli) / Strain (production host): H712 / References: UniProt: P50097, IMP dehydrogenase #2: Chemical | ChemComp-K / #3: Chemical | ChemComp-MZP / #4: Chemical | ChemComp-TRS / #5: 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: 2.64 Å3/Da / Density % sol: 53.37 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.25 Details: PEG 10,000, MES, Glycerol, KCl, Tris, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging 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: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 23, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 117771 / Num. obs: 114993 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 16 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 22 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 7.8 / Num. unique all: 11629 / % possible all: 99.9 |
Reflection | *PLUS Num. obs: 113342 / Num. measured all: 1775920 |
Reflection shell | *PLUS % possible obs: 99.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Tetramer of IMP dehydrogenase, PDB entry 1LRT Resolution: 2→29.71 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.1099 Å2 / ksol: 0.39474 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→29.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 8 Å / Num. reflection Rfree: 11341 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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