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Yorodumi- PDB-5kde: Inorganic pyrophosphatase from Mycobacterium tuberculosis in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kde | ||||||
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Title | Inorganic pyrophosphatase from Mycobacterium tuberculosis in complex with inhibitor 1 and inorganic pyrophosphate | ||||||
Components | Inorganic pyrophosphatase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / hydrolase / pyrophosphatase / drug target / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / host cell surface / magnesium ion binding / extracellular region / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Pang, A.H. / Garzan, A. / Garneau-Tsodikova, S. / Tsodikov, O.V. | ||||||
Citation | Journal: ACS Chem. Biol. / Year: 2016 Title: Discovery of Allosteric and Selective Inhibitors of Inorganic Pyrophosphatase from Mycobacterium tuberculosis. Authors: Pang, A.H. / Garzan, A. / Larsen, M.J. / McQuade, T.J. / Garneau-Tsodikova, S. / Tsodikov, O.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kde.cif.gz | 48.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kde.ent.gz | 32.8 KB | Display | PDB format |
PDBx/mmJSON format | 5kde.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/5kde ftp://data.pdbj.org/pub/pdb/validation_reports/kd/5kde | HTTPS FTP |
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-Related structure data
Related structure data | 5kdfC 4z72S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 19454.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The expressed sequence includes a hexahistidine tag. Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: ppa, Rv3628, MTCY15C10.24 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WI55, inorganic diphosphatase |
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#2: Chemical | ChemComp-6RT / |
#3: Chemical | ChemComp-POP / |
#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: 3.62 Å3/Da / Density % sol: 65.99 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES pH 7.5, 1.6 M NaH2PO4, and 0.2 M KH2PO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Oct 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. obs: 8828 / % possible obs: 99.6 % / Redundancy: 6.8 % / Net I/σ(I): 29 |
Reflection shell | Resolution: 2.65→2.72 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Z72 Resolution: 2.65→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.639 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.359 / ESU R Free: 0.257 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.261 Å2
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Refinement step | Cycle: 1 / Resolution: 2.65→50 Å
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Refine LS restraints |
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