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Yorodumi- PDB-2hf7: Transition State Analogue of AphA class B Acid Phosphatase/Phosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hf7 | ||||||
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Title | Transition State Analogue of AphA class B Acid Phosphatase/Phosphotransferase (Aluminium Fluoride Complex) | ||||||
Components | Class B acid phosphatase | ||||||
Keywords | HYDROLASE / Apha class B Acid phosphatase/phosphotransferase - Transition state analogue | ||||||
Function / homology | Function and homology information L-phosphoserine phosphatase activity / acid phosphatase / acid phosphatase activity / outer membrane-bounded periplasmic space / magnesium ion binding / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Leone, R. / Calderone, V. / Cappelletti, E. / Benvenuti, M. / Mangani, S. | ||||||
Citation | #1: Journal: J.Mol.Biol. / Year: 2004 Title: The First Structure of a Bacterial Class B Acid Phosphatase Reveals Further Structural Heterogeneity Among Phosphatases of Haloacid Deahalogenase Fold Authors: Calderone, V. / Forleo, C. / Benvenuti, M. / Thaller, M.C. / Rossolini, G.M. / Mangani, S. #2: Journal: Biochim.Biophys.Acta / Year: 2006 Title: Biochemical Characterization of the Class B Acid Phosphatase (Apha) of Escherichia Coli Mg1655 Authors: Passariello, C. / Forleo, C. / Micheli, V. / Schippa, S. / Leone, R. / Mangani, S. / Thaller, M.C. / Rossolini, G.M. #3: Journal: J.Mol.Biol. / Year: 2006 Title: A Structure-Based Proposal for the Catalytic Mechanism of Bacterial Acid Phosphatase Apha Belonging to the Dddd Superfamily of Phosphohydrolases Authors: Calderone, V. / Forleo, C. / Benvenuti, M. / Thaller, M.C. / Rossolini, G.M. / Mangani, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hf7.cif.gz | 110.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hf7.ent.gz | 83 KB | Display | PDB format |
PDBx/mmJSON format | 2hf7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hf/2hf7 ftp://data.pdbj.org/pub/pdb/validation_reports/hf/2hf7 | HTTPS FTP |
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-Related structure data
Related structure data | 2b82S 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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Details | The biological assembly is a homotetramer. |
-Components
#1: Protein | Mass: 23468.264 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aphA, napA / Plasmid: pATAC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P0AE22, acid phosphatase #2: Chemical | #3: Chemical | #4: 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: 2.56 Å3/Da / Density % sol: 51.88 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: Reservoior: Na acetate 50mM, 18% (w/v) PEG6000, 0.6% (w/v) Spermine. Protein concentration: 4.16 mg/ml, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 279K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939239 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2006 |
Radiation | Monochromator: Khozu monochromator with a McLennon controller containing a LN2 cooled Si111 crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939239 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→51.16 Å / Num. obs: 62575 / Redundancy: 7.2 % / Rmerge(I) obs: 0.093 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.448 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB code: 2B82 Resolution: 1.6→51.16 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. IN BOTH CHAINS THE AL ATOM OF THE ALUMINIUM TRIFLUORIDE MOLECULE (AF3) IS LINKED BY A COORDINATION BOND TO ASP44 OD1 AND TO A WATER ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. IN BOTH CHAINS THE AL ATOM OF THE ALUMINIUM TRIFLUORIDE MOLECULE (AF3) IS LINKED BY A COORDINATION BOND TO ASP44 OD1 AND TO A WATER MOLECULE (A611 IN CHAIN A AND B612 IN CHAIN B). SINCE THERE IS NO DETECTABLE ELECTRON DENSITY HETEROGENEITY BETWEEN ALUMINIUM TRIFLUORIDE AND ALUMINIUM TETRAFLUORIDE, BOTH WATER MOLECULES, A611 AND A612, COULD BE FLUORINE ATOM.
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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: 11.868 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→51.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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