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Yorodumi- PDB-5kdf: Inorganic pyrophosphatase from Mycobacterium tuberculosis in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kdf | ||||||
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Title | Inorganic pyrophosphatase from Mycobacterium tuberculosis in complex with inhibitor 6 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: 2.45 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 | 5kdf.cif.gz | 50.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kdf.ent.gz | 33.5 KB | Display | PDB format |
PDBx/mmJSON format | 5kdf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kdf_validation.pdf.gz | 755.7 KB | Display | wwPDB validaton report |
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Full document | 5kdf_full_validation.pdf.gz | 757.5 KB | Display | |
Data in XML | 5kdf_validation.xml.gz | 9 KB | Display | |
Data in CIF | 5kdf_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/5kdf ftp://data.pdbj.org/pub/pdb/validation_reports/kd/5kdf | HTTPS FTP |
-Related structure data
Related structure data | 5kdeC 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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1 |
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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 sequence contains 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-6RU / ~{ | ||||
#3: Chemical | #4: Chemical | ChemComp-POP / | #5: 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: 3.55 Å3/Da / Density % sol: 65.31 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.75 1.4 M K H2PO4 2 mM CaCl2 |
-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: Dec 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. obs: 10662 / % possible obs: 97.7 % / Redundancy: 11.8 % / Net I/σ(I): 29 |
Reflection shell | Resolution: 2.45→2.49 Å / Redundancy: 12.2 % / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Z72 Resolution: 2.45→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.052 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.199 / 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: 45.756 Å2
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Refinement step | Cycle: 1 / Resolution: 2.45→50 Å
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Refine LS restraints |
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