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Yorodumi- PDB-1b3o: TERNARY COMPLEX OF HUMAN TYPE-II INOSINE MONOPHOSPHATE DEHYDROGEN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b3o | ||||||
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Title | TERNARY COMPLEX OF HUMAN TYPE-II INOSINE MONOPHOSPHATE DEHYDROGENASE WITH 6-CL-IMP AND SELENAZOLE ADENINE DINUCLEOTIDE | ||||||
Components | PROTEIN (INOSINE MONOPHOSPHATE DEHYDROGENASE 2) | ||||||
Keywords | DEHYDROGENASE / IMPD / IMPDH / GUANINE NUCLEOTIDE SYNTHESIS | ||||||
Function / homology | Function and homology information 'de novo' XMP biosynthetic process / lymphocyte proliferation / Purine ribonucleoside monophosphate biosynthesis / IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / Azathioprine ADME / peroxisomal membrane / GTP biosynthetic process / cellular response to interleukin-4 ...'de novo' XMP biosynthetic process / lymphocyte proliferation / Purine ribonucleoside monophosphate biosynthesis / IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / Azathioprine ADME / peroxisomal membrane / GTP biosynthetic process / cellular response to interleukin-4 / circadian rhythm / secretory granule lumen / ficolin-1-rich granule lumen / Potential therapeutics for SARS / nucleotide binding / Neutrophil degranulation / DNA binding / RNA binding / extracellular exosome / extracellular region / membrane / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Colby, T.D. / Vanderveen, K. / Strickler, M.D. / Goldstein, B.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 Title: Crystal structure of human type II inosine monophosphate dehydrogenase: implications for ligand binding and drug design. Authors: Colby, T.D. / Vanderveen, K. / Strickler, M.D. / Markham, G.D. / Goldstein, B.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b3o.cif.gz | 154.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b3o.ent.gz | 119.6 KB | Display | PDB format |
PDBx/mmJSON format | 1b3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/1b3o ftp://data.pdbj.org/pub/pdb/validation_reports/b3/1b3o | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.371142, 0.928575, -0.001499), Vector: Details | THE BIOLOGICAL UNIT IS A HOMOTETRAMER. IT IS GENERATED BY A CRYSTALLOGRAPHIC FOURFOLD OPERATION ON MONOMER A (OR MONOMER B), NOT BY A SINGLE OPERATION ON BOTH. | |
-Components
#1: Protein | Mass: 55874.863 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Variant: TYPE II ISOZYME / Production host: Escherichia coli (E. coli) / References: UniProt: P12268, IMP dehydrogenase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-UNX / #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: 3.9 Å3/Da / Density % sol: 68.93 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: SEE PRIMARY REFERENCE , pH 8.0 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.91 |
Detector | Type: CORNELL / Detector: CCD / Date: Aug 1, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→100 Å / Num. obs: 34001 / % possible obs: 86.4 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 39.3 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 3 / Rsym value: 0.338 / % possible all: 56 |
Reflection | *PLUS Num. measured all: 126775 |
Reflection shell | *PLUS % possible obs: 56.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CORE DOMAIN OF IMPDH MONOMER FROM HAMSTER IMPD/IMP/MPA COMPLEX STRUCTURE Resolution: 2.9→100 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 182886.58 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED MONOMER B IS THE MORE COMPLETE MONOMER IN THE ASYMMETRIC UNIT, WITH 410 OF 514 RESIDUES FITTED.
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Solvent computation | Solvent model: FLAT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.244 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 3 Å |