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Open data
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Basic information
Entry | Database: PDB / ID: 2ipb | ||||||
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Title | Crystal structure of T159D mutant of S. Typhimurium PhoN protein | ||||||
![]() | Class A nonspecific acid phosphatase PhoN | ||||||
![]() | HYDROLASE / Class-A bacterial non-specific acid phosphatase / T159D mutant of the PhoN protein | ||||||
Function / homology | ![]() acid phosphatase / acid phosphatase activity / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Makde, R.D. / Kumar, V. | ||||||
![]() | ![]() Title: Structure and Mutational Analysis of the PhoN Protein of Salmonella typhimurium Provide Insight into Mechanistic Details Authors: Makde, R.D. / Mahajan, S.K. / Kumar, V. #1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2003 Title: Purification, crystallization and preliminary X-ray diffraction studies of recombinant class A non-specific acid phosphatase of Salmonella typhimurium Authors: Makde, R.D. / Kumar, V. / Rao, A.S. / Yadava, V.S. / Mahajan, S.K. #2: Journal: Biomol.Eng. / Year: 2006 Title: Protein engineering of class-A non-specific acid phosphatase (PhoN) of Salmonella typhimurium: modulation of the pH-activity profile Authors: Makde, R.D. / Dikshit, K. / Kumar, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184.6 KB | Display | ![]() |
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PDB format | ![]() | 148.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.3 KB | Display | ![]() |
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Full document | ![]() | 449.5 KB | Display | |
Data in XML | ![]() | 33.4 KB | Display | |
Data in CIF | ![]() | 47.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2a96SC ![]() 2akcC 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | A dimer is the known biologically active state of the PhoN protein of Salmonella Typhimurium. The entry contains crystallographic asymmetric unit consisting of four chains (two dimers). Chains A and B form one dimer while chains C and D form the other dimer in the asymmetric unit. |
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Components
#1: Protein | Mass: 26163.316 Da / Num. of mol.: 4 / Mutation: T159D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 15% PEG-6000, 25mM potassium chloride, 5mM magnesium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 10, 2005 / Details: mirrors |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→30 Å / Num. all: 43054 / Num. obs: 43054 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.21→2.33 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 4.7 / Num. unique all: 4944 / % possible all: 75.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2A96 Resolution: 2.23→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.322 / SU ML: 0.136 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.271 / ESU R Free: 0.2 / Stereochemistry target values: Engh & Huber
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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: Babinet model with mask | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.06 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.23→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.232→2.29 Å
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