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Yorodumi- PDB-5j5r: M. thermoresistible GuaB2 delta-CBS in complex with inhibitor VCC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j5r | ||||||||||||
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Title | M. thermoresistible GuaB2 delta-CBS in complex with inhibitor VCC234718 | ||||||||||||
Components | Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase | ||||||||||||
Keywords | OXIDOREDUCTASE / inhibitor / IMPDH / mycobacterium / GuaB2 | ||||||||||||
Function / homology | Function and homology information IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / nucleotide binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Mycobacterium thermoresistibile ATCC 19527 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||||||||
Authors | Pacitto, A. / Ascher, D.B. / Blundell, T.L. | ||||||||||||
Funding support | United Kingdom, Australia, 3items
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Citation | Journal: ACS Infect Dis / Year: 2017 Title: The Inosine Monophosphate Dehydrogenase, GuaB2, Is a Vulnerable New Bactericidal Drug Target for Tuberculosis. Authors: Singh, V. / Donini, S. / Pacitto, A. / Sala, C. / Hartkoorn, R.C. / Dhar, N. / Keri, G. / Ascher, D.B. / Mondesert, G. / Vocat, A. / Lupien, A. / Sommer, R. / Vermet, H. / Lagrange, S. / ...Authors: Singh, V. / Donini, S. / Pacitto, A. / Sala, C. / Hartkoorn, R.C. / Dhar, N. / Keri, G. / Ascher, D.B. / Mondesert, G. / Vocat, A. / Lupien, A. / Sommer, R. / Vermet, H. / Lagrange, S. / Buechler, J. / Warner, D.F. / McKinney, J.D. / Pato, J. / Cole, S.T. / Blundell, T.L. / Rizzi, M. / Mizrahi, V. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j5r.cif.gz | 78.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j5r.ent.gz | 60.8 KB | Display | PDB format |
PDBx/mmJSON format | 5j5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/5j5r ftp://data.pdbj.org/pub/pdb/validation_reports/j5/5j5r | 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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Unit cell |
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-Components
#1: Protein | Mass: 39854.477 Da / Num. of mol.: 1 / Fragment: UNP residues 2-109, 237-513 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium thermoresistibile ATCC 19527 (bacteria) Gene: KEK_23061 / Production host: Escherichia coli (E. coli) / References: UniProt: G7CNL4, IMP dehydrogenase |
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#2: Chemical | ChemComp-6G1 / |
#3: Chemical | ChemComp-IMP / |
#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: 2.13 Å3/Da / Density % sol: 42.17 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: sodium acetate, calcium chloride, iso-propanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→44.7 Å / Num. obs: 43941 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 12.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→44.68 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.65
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→44.68 Å
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Refine LS restraints |
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LS refinement shell |
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