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Yorodumi- PDB-1nfb: Ternary complex of the human type II Inosine Monophosphate Dedhyd... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nfb | ||||||
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Title | Ternary complex of the human type II Inosine Monophosphate Dedhydrogenase with 6Cl-IMP and NAD | ||||||
Components | Inosine-5'-monophosphate dehydrogenase 2 | ||||||
Keywords | OXIDOREDUCTASE / 8 STRANDED PARALLE ALPHA/BETA BARREL / DEHYDROGENASE / IMPD / IMPDH / GUANINE NUCLEOTIDE BIOSYNTHESIS NAD | ||||||
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 / Potential therapeutics for SARS / secretory granule lumen / ficolin-1-rich granule lumen / nucleotide binding / Neutrophil degranulation / DNA binding / RNA binding / extracellular exosome / extracellular region / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Risal, D. / Strickler, M.D. / Goldstein, B.M. | ||||||
Citation | Journal: To be Published Title: The Conformation of NAD Bound to Human Inosine Monophosphate Dehydrogenase Type II Authors: Risal, D. / Strickler, M.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 | 1nfb.cif.gz | 164.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nfb.ent.gz | 127.2 KB | Display | PDB format |
PDBx/mmJSON format | 1nfb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nfb_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1nfb_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1nfb_validation.xml.gz | 36 KB | Display | |
Data in CIF | 1nfb_validation.cif.gz | 48.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/1nfb ftp://data.pdbj.org/pub/pdb/validation_reports/nf/1nfb | HTTPS FTP |
-Related structure data
Related structure data | 1b3oS 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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2 |
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Unit cell |
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-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) / Gene: IMPDH2 / Plasmid: pET12B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P12268, IMP dehydrogenase #2: Chemical | #3: Chemical | #4: 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: 4.06 Å3/Da / Density % sol: 69.5 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 8% PEG 6000, 0.1M Tris-HCl, 24mM beta-mercaptoethanol, 1M LiCl, 20% Glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.93 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 2002 / Details: mirrors |
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→51.33 Å / Num. all: 29280 / Num. obs: 24775 / % possible obs: 85.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 39.8 Å2 / Rmerge(I) obs: 0.034 / Rsym value: 0.034 / Net I/σ(I): 17.37 |
Reflection shell | Resolution: 2.9→2.98 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1757 / Rsym value: 0.343 / % possible all: 81 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Chain A of PDB ENTRY 1B3O Resolution: 2.9→47.82 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.1 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.7494 Å2 / ksol: 0.344832 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→47.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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