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Yorodumi- PDB-5upu: Crystal Structure of the Catalytic Domain of the Inosine Monophos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5upu | ||||||
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Title | Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Mycobacterium tuberculosis in the presence of TBK6 | ||||||
Components | Inosine-5'-monophosphate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / IMPDH / delta CBS / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | Function and homology information XMP biosynthetic process / IMP catabolic process / IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / peptidoglycan-based cell wall / nucleotide binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.905 Å | ||||||
Authors | Kim, Y. / Makowska-Grzyska, M. / Maltseva, N. / Mulligan, R. / Gu, M. / Sacchettini, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Mycobacterium tuberculosis in the presence of TBK6 Authors: Kim, Y. / Makowska-Grzyska, M. / Maltseva, N. / Mulligan, R. / Gu, M. / Sacchettini, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5upu.cif.gz | 77.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5upu.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 5upu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/5upu ftp://data.pdbj.org/pub/pdb/validation_reports/up/5upu | HTTPS FTP |
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-Related structure data
Related structure data | 5uqhC 4zqrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 41642.621 Da / Num. of mol.: 1 Mutation: CBS domain (residues 126-252) is replaced by GGLLV Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: guaB, guaB2, Rv3411c, MTCY78.17 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: P9WKI7, IMP dehydrogenase |
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#2: Chemical | ChemComp-IMP / |
#3: Chemical | ChemComp-6Q9 / ~{ |
#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 Å3/Da / Density % sol: 38.65 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M imidazole pH 8.0, 2.5 M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 7281 / % possible obs: 99.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.077 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 352 / CC1/2: 0.643 / Rsym value: 0.672 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZQR Resolution: 2.905→35.922 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.49
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.905→35.922 Å
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Refine LS restraints |
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LS refinement shell |
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