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- PDB-1n8n: Crystal structure of the Au3+ complex of AphA class B acid phosph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1n8n | ||||||
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Title | Crystal structure of the Au3+ complex of AphA class B acid phosphatase/phosphotransferase from E. coli at 1.69 A resolution | ||||||
![]() | Class B acid phosphatase | ||||||
![]() | HYDROLASE / Class B acid phosphatase / DDDD acid phosphatase / metallo-enzyme | ||||||
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. / Rossolini, G.M. / Thaller, M.C. / Mangani, S. | ||||||
![]() | ![]() 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. #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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.6 KB | Display | ![]() |
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PDB format | ![]() | 44.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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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Components on special symmetry positions |
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Details | The biological assembly is a tetramer |
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Components
#1: Protein | Mass: 23555.342 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P32697, UniProt: P0AE22*PLUS, acid phosphatase |
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#2: Chemical | ChemComp-AU3 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.16 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: AphA 6mg/mL, 50 mM Na acetate, 25% PEG 6000, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K. The crystals of the native enzyme (containing Mg2+ or Zn2+) have been soaked in 1 mM solution of AuCl3 | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 13, 2002 / Details: Toroidal mirror | ||||||||||||
Radiation | Monochromator: Double crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.69→46.13 Å / Num. all: 31884 / Num. obs: 31884 / % possible obs: 88.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 19.709 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 7 | ||||||||||||
Reflection shell | Resolution: 1.69→1.79 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.093 / Mean I/σ(I) obs: 7 / Num. unique all: 2976 / Rsym value: 0.093 / % possible all: 53 | ||||||||||||
Reflection | *PLUS Lowest resolution: 25 Å / % possible obs: 98.2 % / Redundancy: 4.3 % / Num. measured all: 135549 / Rmerge(I) obs: 0.075 | ||||||||||||
Reflection shell | *PLUS % possible obs: 92 % / Redundancy: 2.9 % / Num. unique obs: 2579 / Num. measured obs: 7369 / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 1.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: MAD-phased Bromine derivative at 2.2 A resolution Resolution: 1.69→46.13 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Shrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.602 Å2
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Refine analyze | Luzzati sigma a obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.69→46.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.69→1.79 Å / Total num. of bins used: 20
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Refinement | *PLUS Lowest resolution: 25 Å / Rfactor Rfree: 0.207 / Rfactor Rwork: 0.178 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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