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Yorodumi- PDB-4z72: Crystal structure of inorganic pyrophosphatase from Mycobacterium... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4z72 | ||||||
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Title | Crystal structure of inorganic pyrophosphatase from Mycobacterium tuberculosis in complex with two phosphate ions | ||||||
Components | Inorganic pyrophosphatase | ||||||
Keywords | HYDROLASE / PYROPHOSPHATASE / PHOSPHATASE / INORGANIC PYROPHOSPHATE | ||||||
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: 2.352 Å | ||||||
Authors | Pratt, A.C. / Biswas, T. / Barnard-Britson, S. / Tsodikov, O.V. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2015 Title: Structural and computational dissection of the catalytic mechanism of the inorganic pyrophosphatase from Mycobacterium tuberculosis. Authors: Pratt, A.C. / Dewage, S.W. / Pang, A.H. / Biswas, T. / Barnard-Britson, S. / Cisneros, G.A. / 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 | 4z72.cif.gz | 49.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z72.ent.gz | 33.1 KB | Display | PDB format |
PDBx/mmJSON format | 4z72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4z72_validation.pdf.gz | 431.7 KB | Display | wwPDB validaton report |
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Full document | 4z72_full_validation.pdf.gz | 431.7 KB | Display | |
Data in XML | 4z72_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 4z72_validation.cif.gz | 10.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/4z72 ftp://data.pdbj.org/pub/pdb/validation_reports/z7/4z72 | HTTPS FTP |
-Related structure data
Related structure data | 4z70C 4z71SC 4z73C 4z74C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 19454.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: ppa, Rv3628, MTCY15C10.24 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WI55, inorganic diphosphatase | ||||
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#2: Chemical | #3: Chemical | #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: 3.54 Å3/Da / Density % sol: 65.25 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: reservoir: 1.6 M KH2PO4, 100 mM HEPES pH 7.75 and 2 mM CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 11538 / % possible obs: 99.3 % / Redundancy: 7.1 % / Net I/σ(I): 18.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Z71 Resolution: 2.352→40 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.556 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.437 Å2
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Refinement step | Cycle: 1 / Resolution: 2.352→40 Å
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Refine LS restraints |
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