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Yorodumi- PDB-1rmt: Crystal structure of AphA class B acid phosphatase/phosphotransfe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rmt | ||||||
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Title | Crystal structure of AphA class B acid phosphatase/phosphotransferase complexed with adenosine. | ||||||
Components | Class B acid phosphatase | ||||||
Keywords | HYDROLASE / Class B acid phosphatase / DDDD acid phosphatase / metallo-enzyme / adenosine. | ||||||
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 / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Calderone, V. / Forleo, C. / Benvenuti, M. / Rossolini, G.M. / Thaller, M.C. / Mangani, S. | ||||||
Citation | Journal: To be Published Title: Insights in the catalytic mechanism of AphA from Escherichia coli Authors: Calderone, V. / Forleo, C. / Benvenuti, M. / Rossolini, G.M. / Thaller, M.C. / Mangani, S. #1: Journal: FEMS Microbiol.Lett. / Year: 1997 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: Journal: Acta Crystallogr.,Sect.D / Year: 2003 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. / M Rossolini, G. / Mangani, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rmt.cif.gz | 383.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rmt.ent.gz | 308.8 KB | Display | PDB format |
PDBx/mmJSON format | 1rmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rmt_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1rmt_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 1rmt_validation.xml.gz | 46.9 KB | Display | |
Data in CIF | 1rmt_validation.cif.gz | 70.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rm/1rmt ftp://data.pdbj.org/pub/pdb/validation_reports/rm/1rmt | HTTPS FTP |
-Related structure data
Related structure data | 1rmqC 1rmyC 1n8nS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | The biological assembly is a tetramer and there is a tetramer in the asymmetric unit. |
-Components
#1: Protein | Mass: 23555.342 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: APHA, NAPA, B4055, SF4149, S3580 / Plasmid: pATac / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha References: UniProt: P32697, UniProt: P0AE22*PLUS, acid phosphatase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-ADN / #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: 2.36 Å3/Da / Density % sol: 47.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: Crystallization components* AphA 6mg/mL, 50mM Na acetate, 25% PEG 6000, 10mM adenosine, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.96111 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 7, 2002 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96111 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→75.419 Å / Num. all: 153897 / Num. obs: 153897 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 3.7 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.452 / % possible all: 59.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1N8N Resolution: 1.4→74.54 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.205 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.067 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.611 Å2
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Refine analyze | Luzzati coordinate error obs: 0.046 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→74.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20 /
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