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Yorodumi- PDB-4zqp: Crystal Structure of the Catalytic Domain of the Inosine Monophos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zqp | ||||||
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Title | Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Mycobacterium tuberculosis in the complex with IMP and the inhibitor MAD1 | ||||||
Components | Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase | ||||||
Keywords | Oxidoreductase/Oxidoreductase inhibitor / IMPDH / delta CBS / MAD1 / Structural Genomics / Center for Membrane Proteins of Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / 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: 1.9 Å | ||||||
Authors | Kim, Y. / Makowska-Grzyska, M. / Gu, M. / Kavitha, M. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: Plos One / Year: 2015 Title: Mycobacterium tuberculosis IMPDH in Complexes with Substrates, Products and Antitubercular Compounds. Authors: Makowska-Grzyska, M. / Kim, Y. / Gorla, S.K. / Wei, Y. / Mandapati, K. / Zhang, M. / Maltseva, N. / Modi, G. / Boshoff, H.I. / Gu, M. / Aldrich, C. / Cuny, G.D. / Hedstrom, L. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zqp.cif.gz | 153.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zqp.ent.gz | 117 KB | Display | PDB format |
PDBx/mmJSON format | 4zqp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/4zqp ftp://data.pdbj.org/pub/pdb/validation_reports/zq/4zqp | HTTPS FTP |
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-Related structure data
Related structure data | 4zqmC 4zqnC 4zqoC 4zqrC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 41642.621 Da / Num. of mol.: 1 Fragment: UNP residues 1-125 and 253-529 linked by linker (GLY GLY) 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) gold / References: UniProt: P9WKI7, IMP dehydrogenase |
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-Non-polymers , 7 types, 175 molecules
#2: Chemical | ChemComp-IMP / |
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#3: Chemical | ChemComp-KP3 / |
#4: Chemical | ChemComp-K / |
#5: Chemical | ChemComp-PO4 / |
#6: Chemical | ChemComp-GOL / |
#7: Chemical | ChemComp-PGO / |
#8: 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: 1.98 Å3/Da / Density % sol: 37.79 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 0.1 M Na/K phosphate pH 6.2, 25 %(v/v) 1,2 propandiol, 10 %(v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97899 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2013 |
Radiation | Monochromator: double crystal monochrimator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97899 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→35.76 Å / Num. obs: 25094 / % possible obs: 97 % / Redundancy: 3.8 % / Biso Wilson estimate: 22.26 Å2 / Rsym value: 0.103 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 1.84 / % possible all: 78.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→35.76 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.81 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→35.76 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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