+Open data
-Basic information
Entry | Database: PDB / ID: 6k21 | ||||||
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Title | Pyrophosphatase from Acinetobacter baumannii | ||||||
Components | Inorganic pyrophosphatase | ||||||
Keywords | HYDROLASE / Pyrophosphatase from Acinetobacter baumannii | ||||||
Function / homology | Function and homology information inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Su, J. | ||||||
Citation | Journal: Int J Mol Sci / Year: 2019 Title: Crystal Structures of Pyrophosphatase from Acinetobacter baumannii: Snapshots of Pyrophosphate Binding and Identification of a Phosphorylated Enzyme Intermediate. Authors: Si, Y. / Wang, X. / Yang, G. / Yang, T. / Li, Y. / Ayala, G.J. / Li, X. / Wang, H. / Su, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k21.cif.gz | 53.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k21.ent.gz | 36.5 KB | Display | PDB format |
PDBx/mmJSON format | 6k21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/6k21 ftp://data.pdbj.org/pub/pdb/validation_reports/k2/6k21 | HTTPS FTP |
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-Related 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: 19503.141 Da / Num. of mol.: 1 / Mutation: A139S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: ppa / Production host: Escherichia coli (E. coli) References: UniProt: N9S5K0, UniProt: A0A333SMX2*PLUS, inorganic diphosphatase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
Source details | The protein was from a strain of Acinetobacter baumannii from a hospital. The sequence reference ...The protein was from a strain of Acinetobacter baumannii from a hospital. The sequence reference used is from a different species Acinetobacter ursingii NIPH 706. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.03 Å3/Da / Density % sol: 69.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: malic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→19.9 Å / Num. obs: 21726 / % possible obs: 99.8 % / Redundancy: 9.8 % / Net I/σ(I): 9 |
Reflection shell | Resolution: 2→2.05 Å / Num. unique obs: 1576 |
-Processing
Software | Name: PHENIX / Version: 1.12_2829 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.897 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.77 / 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 max: 63.11 Å2 / Biso mean: 25.6826 Å2 / Biso min: 10.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→19.897 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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