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- PDB-1z88: Crystal structure of Lys154Arg mutant of mature AphA of S. typhimurium -
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Open data
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Basic information
Entry | Database: PDB / ID: 1z88 | ||||||
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Title | Crystal structure of Lys154Arg mutant of mature AphA of S. typhimurium | ||||||
![]() | AphA protein | ||||||
![]() | HYDROLASE / Class-B bacterial acid phosphatase / Lys154Arg mutant of mature AphA / metalloenzyme | ||||||
Function / homology | ![]() acid phosphatase / acid phosphatase activity / outer membrane-bounded periplasmic space / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Makde, R.D. / Gupta, G.D. / Kumar, V. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184.5 KB | Display | ![]() |
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PDB format | ![]() | 146.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.2 KB | Display | ![]() |
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Full document | ![]() | 457.8 KB | Display | |
Data in XML | ![]() | 35.8 KB | Display | |
Data in CIF | ![]() | 51.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1z5gSC ![]() 2autC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23898.717 Da / Num. of mol.: 4 / Mutation: K154R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P58683, UniProt: Q540U1*PLUS, acid phosphatase #2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.7 Details: PEG 6000, magnesium chloride, sodium acetate, glycerol, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 24, 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: 2.1→30 Å / Num. all: 47811 / Num. obs: 47808 / % possible obs: 91.3 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 5.2 / Num. unique all: 6600 / % possible all: 87.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1Z5G Resolution: 2.1→20 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: Flat Model / Bsol: 47.9 Å2 / ksol: 0.34 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.3 Å2 | |||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.17 Å / Total num. of bins used: 10
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Xplor file |
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