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Yorodumi- PDB-2aut: Crystal structure of Lys154Asn mutant of mature AphA of S. typhimurium -
+Open data
-Basic information
Entry | Database: PDB / ID: 2aut | ||||||
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Title | Crystal structure of Lys154Asn mutant of mature AphA of S. typhimurium | ||||||
Components | AphA | ||||||
Keywords | HYDROLASE / Class-B bacterial non-specific acid phosphatase / Lys154Asn mutant of mature AphA / metalloenzyme | ||||||
Function / homology | Function and homology information acid phosphatase / acid phosphatase activity / outer membrane-bounded periplasmic space / metal ion binding Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.25 Å | ||||||
Authors | Makde, R.D. / Gupta, G.D. / Kumar, V. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2007 Title: Structural and mutational analyses reveal the functional role of active-site Lys-154 and Asp-173 of Salmonella typhimurium AphA protein. Authors: Makde, R.D. / Gupta, G.D. / Mahajan, S.K. / Kumar, V. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Expression, purification, crystallization and preliminary X-ray diffraction studies of recombinant class B non-specific acid phosphatase of Salmonella typhimurium Authors: Makde, R.D. / Kumar, V. / Gupta, G.D. / Jasti, J. / Singh, T.P. / Mahajan, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2aut.cif.gz | 185.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2aut.ent.gz | 147.4 KB | Display | PDB format |
PDBx/mmJSON format | 2aut.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2aut_validation.pdf.gz | 461 KB | Display | wwPDB validaton report |
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Full document | 2aut_full_validation.pdf.gz | 467.1 KB | Display | |
Data in XML | 2aut_validation.xml.gz | 36.1 KB | Display | |
Data in CIF | 2aut_validation.cif.gz | 52 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/2aut ftp://data.pdbj.org/pub/pdb/validation_reports/au/2aut | HTTPS FTP |
-Related structure data
Related structure data | 1z5gSC 1z88C 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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1 |
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Unit cell |
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Details | The entry contains the crystallographic asymmetric unit consisting of four chains (homotetramer), which is the known biologically active state of the APHA protein. |
-Components
#1: Protein | Mass: 23855.625 Da / Num. of mol.: 4 / Mutation: K154N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: aphA / Plasmid: pET21(A) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P58683, UniProt: Q540U1*PLUS, acid phosphatase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-PO4 / | #5: 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: 2.34 Å3/Da / Density % sol: 47.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion sitting-drop, micro-seeding / pH: 4.7 Details: PEG 6000, magnesium chloride, sodium acetate, dihydrogen phosphate , pH 4.7, vapour diffusion sitting-drop, micro-seeding, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 31, 2004 / Details: OSMIC mirror |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→30 Å / Num. all: 40809 / Num. obs: 40671 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 24.77 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.24→2.36 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 7.1 / Num. unique all: 5241 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: Partially refined structure of wild-type APHA (PDB code 1Z5G) with all HET atoms (HOH, MG etc.) removed and side chain of Lys154 replaced with ALA was used as the starting model. A ...Starting model: Partially refined structure of wild-type APHA (PDB code 1Z5G) with all HET atoms (HOH, MG etc.) removed and side chain of Lys154 replaced with ALA was used as the starting model. A random error of 0.2A was added to the atomic coordinates of the starting model. Resolution: 2.25→20 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: Flat Model / Bsol: 31.75 Å2 / ksol: 0.327 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.29 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.33 Å / Total num. of bins used: 10
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Xplor file |
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