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Yorodumi- PDB-3cz4: Native AphA class B acid phosphatase/phosphotransferase from E. coli -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cz4 | ||||||
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Title | Native AphA class B acid phosphatase/phosphotransferase from E. coli | ||||||
Components | Class B acid phosphatase | ||||||
Keywords | HYDROLASE / ACID PHOSPHATASE/PHOSPHOTRANSFERASE / METALLO PHOSPHATASE / Magnesium / Metal-binding / Periplasm | ||||||
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: 1.7 Å | ||||||
Authors | Leone, R. / Cappelletti, E. / Benvenuti, M. / Lentini, G. / Thaller, M.C. / Mangani, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structural insights into the catalytic mechanism of the bacterial class B phosphatase AphA belonging to the DDDD superfamily of phosphohydrolases. Authors: Leone, R. / Cappelletti, E. / Benvenuti, M. / Lentini, G. / Thaller, M.C. / Mangani, S. #1: 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 | 3cz4.cif.gz | 65.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cz4.ent.gz | 47.3 KB | Display | PDB format |
PDBx/mmJSON format | 3cz4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cz4_validation.pdf.gz | 439.8 KB | Display | wwPDB validaton report |
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Full document | 3cz4_full_validation.pdf.gz | 441.2 KB | Display | |
Data in XML | 3cz4_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 3cz4_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/3cz4 ftp://data.pdbj.org/pub/pdb/validation_reports/cz/3cz4 | HTTPS FTP |
-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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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23555.342 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: aphA, napA, yjbP, b4055, JW4015 / Plasmid: pATAC / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(De3) / References: UniProt: P0AE22, acid phosphatase |
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-Non-polymers , 5 types, 333 molecules
#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-EDO / #6: 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: 3.34 Å3/Da / Density % sol: 63.17 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: drop: 4.2-3.5 mg/mL in 50 mM CH3COONa buffer at pH 7.2, 10 mM MgCl2 reservoir: 18% (w/v) polyethylene glycol (PEG) 6000, 0.6% (w/v) Spermine, 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: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 13, 2002 Details: Monochromator double crystal, Si(111); toroidal mirror |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→8 Å / Num. obs: 31967 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 17.14 Å2 / Rsym value: 0.092 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 1.7→1.742 Å / Redundancy: 4.14 % / Rmerge(I) obs: 0.165 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2311 / Rsym value: 0.165 / % possible all: 99.51 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2B82 Resolution: 1.7→7.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.728 / SU ML: 0.058 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.092 / ESU R Free: 0.093 / 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: 23.54 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→7.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.742 Å / Total num. of bins used: 20
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