[English] 日本語
Yorodumi- PDB-1jr1: Crystal structure of Inosine Monophosphate Dehydrogenase in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jr1 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Inosine Monophosphate Dehydrogenase in complex with Mycophenolic Acid | ||||||
Components | Inosine-5'-Monophosphate Dehydrogenase 2 | ||||||
Keywords | OXIDOREDUCTASE / DEHYDROGENASE / IMPD / IMPDH / GUANINE NUCLEOTIDE SYNTHESIS / MYCOPHENOLIC ACID / MPA | ||||||
Function / homology | Function and homology information lymphocyte proliferation / IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / cellular response to interleukin-4 / circadian rhythm / nucleotide binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Cricetulus griseus (Chinese hamster) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.6 Å | ||||||
Authors | Sintchak, M.D. / Fleming, M.A. / Futer, O. / Raybuck, S.A. / Chambers, S.P. / Caron, P.R. / Murcko, M.A. / Wilson, K.P. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1996 Title: Structure and mechanism of inosine monophosphate dehydrogenase in complex with the immunosuppressant mycophenolic acid. Authors: Sintchak, M.D. / Fleming, M.A. / Futer, O. / Raybuck, S.A. / Chambers, S.P. / Caron, P.R. / Murcko, M.A. / Wilson, K.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1jr1.cif.gz | 165.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1jr1.ent.gz | 135.8 KB | Display | PDB format |
PDBx/mmJSON format | 1jr1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jr1_validation.pdf.gz | 614.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1jr1_full_validation.pdf.gz | 613.4 KB | Display | |
Data in XML | 1jr1_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 1jr1_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/1jr1 ftp://data.pdbj.org/pub/pdb/validation_reports/jr/1jr1 | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | the biological assembly is a tetramer generated from chain A in the asymmetric unit by the operations: -x,-y,z; -y,x,z; y,-x,z |
-Components
#1: Protein | Mass: 55961.082 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Production host: Escherichia coli (E. coli) / References: UniProt: P12269, IMP dehydrogenase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.43 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: PEG 6000, LiCl, MES, 1-methyl-2-pyrrolidinone, 2-mercaptoethanol, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 1, 1995 |
Radiation | Monochromator: Yale/MSC mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. all: 40314 / Num. obs: 37492 / % possible obs: 93 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rsym value: 5.2 |
Reflection shell | Resolution: 2.6→2.71 Å / % possible all: 80 |
Reflection | *PLUS % possible obs: 93 % / Num. measured all: 123246 / Rmerge(I) obs: 0.052 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 2.6→8 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→8 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.71 Å
| |||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 8 Å / σ(F): 1 / % reflection Rfree: 10 % / Rfactor obs: 0.217 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.317 / % reflection Rfree: 11 % / Rfactor Rwork: 0.276 |