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- PDB-2b8j: Crystal structure of AphA class B acid phosphatase/phosphotransfe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2b8j | |||||||||
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Title | Crystal structure of AphA class B acid phosphatase/phosphotransferase ternary complex with adenosine and phosphate at 2 A resolution | |||||||||
![]() | class B acid phosphatase | |||||||||
![]() | HYDROLASE / Class B acid phosphatase / DDDD acid phosphatase / metallo-enzyme / AMP | |||||||||
Function / homology | ![]() L-phosphoserine phosphatase activity / acid phosphatase / acid phosphatase activity / outer membrane-bounded periplasmic space / magnesium ion binding / identical protein binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Calderone, V. / Forleo, C. / Benvenuti, M. / Thaller, M.C. / Rossolini, G.M. / Mangani, S. | |||||||||
![]() | ![]() 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. #1: ![]() Title: Identification of the gene (aphA) encoding the class B acid phosphatase/phosphotransferase of Escherichia coli MG1655 and characterization of its product Authors: Thaller, M.C. / Schippa, S. / Bonci, A. / Cresti, S. / Rossolini, G.M. #2: ![]() Title: Expression, purification, crystallization and preliminary X-ray characterization of the class B acid phosphatase (AphA) from Escherichia coli Authors: Forleo, C. / Benvenuti, M. / Calderone, V. / Schippa, S. / Docquier, J.D. / Thaller, M.C. / Rossolini, G.M. / Mangani, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.7 KB | Display | ![]() |
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PDB format | ![]() | 76.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2b82C ![]() 1n8nS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | The biological assembly is a tetramer, but there is a dimer in the asymmetric unit |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23468.264 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P32697, UniProt: P0AE22*PLUS, acid phosphatase |
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-Non-polymers , 7 types, 216 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/SPM.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/AU.gif)
![](data/chem/img/AU3.gif)
![](data/chem/img/ADN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SPM.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/AU.gif)
![](data/chem/img/AU3.gif)
![](data/chem/img/ADN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-SPM / | #4: Chemical | ChemComp-PO4 / | #5: Chemical | ChemComp-AU / | #6: Chemical | ChemComp-AU3 / | #7: Chemical | ChemComp-ADN / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 49 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: AphA 6mg/mL, 50 mM Na acetate, 25% PEG 6000, 10mM AMP, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 23, 2003 / Details: Double-crystal monochromator |
Radiation | Monochromator: double-crystal monochromator plus Si(111) and Si(220) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.001 Å / Relative weight: 1 |
Reflection | Resolution: 2.033→49.65 Å / Num. all: 28127 / Num. obs: 28127 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 19.44 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.033→2.14 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 4.2 / Num. unique all: 3767 / Rsym value: 0.147 / % possible all: 89.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1N8N Resolution: 2.033→49.39 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.917 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.199 / ESU R Free: 0.173 / 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: 18.581 Å2
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Refine analyze | Luzzati coordinate error obs: 0.111 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.033→49.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.033→2.086 Å / Total num. of bins used: 20
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