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Yorodumi- PDB-6kcf: Structure of Inosine 5'-monophosphate Dehydrogenase from Candidat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kcf | |||||||||
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Title | Structure of Inosine 5'-monophosphate Dehydrogenase from Candidatus Liberibacter asiaticus str. psy62 | |||||||||
Components | Inosine-5'-monophosphate dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / Inosine 5'-monophosphate Dehydrogenase | |||||||||
Function / homology | Function and homology information IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / nucleotide binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Liberibacter asiaticus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | |||||||||
Authors | Nan, J. / Zhang, S.R. / Jiang, L. | |||||||||
Funding support | China, 2items
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Citation | Journal: Molecules / Year: 2020 Title: Evaluation of Bronopol and Disulfiram as Potential Candidatus Liberibacter asiaticus Inosine 5'-Monophosphate Dehydrogenase Inhibitors by Using Molecular Docking and Enzyme Kinetic. Authors: Nan, J. / Zhang, S. / Zhan, P. / Jiang, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kcf.cif.gz | 217.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kcf.ent.gz | 171.8 KB | Display | PDB format |
PDBx/mmJSON format | 6kcf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/6kcf ftp://data.pdbj.org/pub/pdb/validation_reports/kc/6kcf | 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: 41059.965 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Liberibacter asiaticus (strain psy62) (bacteria) Strain: psy62 / Gene: quaB, guaB, CLIBASIA_03930 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C6XG59, IMP dehydrogenase #2: 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: 2.47 Å3/Da / Density % sol: 50.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 30% PEG 400, 100 mM HEPES pH 7.5, 200 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→42.469 Å / Num. obs: 51023 / % possible obs: 98.2 % / Redundancy: 2.58 % / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 2.55→3 Å / Num. unique obs: 50928 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→42.469 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.3 Å2 / Biso mean: 69.2922 Å2 / Biso min: 29.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.55→42.469 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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