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Yorodumi- PDB-2g1a: Crystal structure of the complex between Apha class B acid phosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g1a | ||||||
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Title | Crystal structure of the complex between Apha class B acid phosphatase/phosphotransferase | ||||||
Components | Class B acid phosphatase | ||||||
Keywords | HYDROLASE / ACID PHOSPHATASE/PHOSPHOTRANSFERASE / METALLO PHOSPHATASE | ||||||
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: 2 Å | ||||||
Authors | Leone, R. / Calderone, V. / Cappelletti, E. / Benvenuti, M. / Mangani, S. | ||||||
Citation | Journal: To be published Title: Crystal structure of the complex between Apha class B acid phosphatase/phosphotransferase Authors: Leone, R. / Calderone, V. / Cappelletti, E. / Benvenuti, M. / Mangani, S. #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 the haloacid dehalogenase fold Authors: Calderone, V. / Forleo, C. / Benvenuti, M. / Thaller, M.C. / Rossolini, G.M. / Mangani, S. #2: Journal: J.Mol.Biol. / Year: 2006 Title: A structure-based proposal for the catalytic mechanism of the 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 | 2g1a.cif.gz | 111.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g1a.ent.gz | 84.2 KB | Display | PDB format |
PDBx/mmJSON format | 2g1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g1a_validation.pdf.gz | 992.7 KB | Display | wwPDB validaton report |
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Full document | 2g1a_full_validation.pdf.gz | 995.1 KB | Display | |
Data in XML | 2g1a_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 2g1a_validation.cif.gz | 37.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/2g1a ftp://data.pdbj.org/pub/pdb/validation_reports/g1/2g1a | HTTPS FTP |
-Related structure data
Related structure data | 1n8nS 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. The asymettric unit contain two subunits. |
-Components
#1: Protein | Mass: 23555.342 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aphA, napA / Production host: Escherichia coli (E. coli) / 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: 2.54 Å3/Da / Density % sol: 51.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: Drop: aphA 6mg/ml, MG2+ 10mM, PMEA 10mM. Reservoir solution: 50mM Na acetate, 0.6% (w/v) Spermine tetrahydrochloride, 22% PEG6000, pH7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 3, 2005 |
Radiation | Monochromator: Diamond (111), Ge (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2→50.7 Å / Num. obs: 30906 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 |
Reflection shell | Resolution: 2→2.11 Å / Rmerge(I) obs: 0.036 / % possible all: 79.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB code 1N8N Resolution: 2→50.7 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.911 / SU B: 3.321 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.188 / ESU R Free: 0.156 / 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: 10.313 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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