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Open data
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Basic information
Entry | Database: PDB / ID: 5xlv | ||||||
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Title | Mycobacterium tuberculosis Pantothenate kinase mutant F254A | ||||||
![]() | Pantothenate kinase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Paul, A. / Kumar, P. / Surolia, A. / Vijayan, M. | ||||||
![]() | ![]() Title: Biochemical and structural studies of mutants indicate concerted movement of the dimer interface and ligand-binding region of Mycobacterium tuberculosis pantothenate kinase Authors: Paul, A. / Kumar, P. / Surolia, A. / Vijayan, M. #1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. Year: 2005 Title: Expression, purification, crystallization and preliminary X-ray crystallographic analysis of pantothenate kinase from Mycobacterium tuberculosis. Authors: Das, S. / Kumar, P. / Bhor, V. / Surolia, A. / Vijayan, M. #2: ![]() Title: Invariance and variability in bacterial PanK: a study based on the crystal structure of Mycobacterium tuberculosis PanK. Authors: Das, S. / Kumar, P. / Bhor, V. / Surolia, A. / Vijayan, M. #3: ![]() Title: Mycobacterium tuberculosis pantothenate kinase: possible changes in location of ligands during enzyme action. Authors: Chetnani, B. / Das, S. / Kumar, P. / Surolia, A. / Vijayan, M. #4: ![]() Title: M. tuberculosis pantothenate kinase: dual substrate specificity and unusual changes in ligand locations. Authors: Chetnani, B. / Kumar, P. / Surolia, A. / Vijayan, M. #5: ![]() Title: Location and conformation of pantothenate and its derivatives in Mycobacterium tuberculosis pantothenate kinase: insights into enzyme action. Authors: Chetnani, B. / Kumar, P. / Abhinav, K.V. / Chhibber, M. / Surolia, A. / Vijayan, 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 | ![]() | 154.5 KB | Display | ![]() |
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PDB format | ![]() | 120.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5xlwC ![]() 5xmbC ![]() 2geuS C: citing same article ( S: Starting model for refinement |
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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 on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | ![]() Mass: 35628.754 Da / Num. of mol.: 2 / Mutation: F254A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 25618 / H37Rv / Gene: coaA, Rv1092c, MTV017.45c / Plasmid: PET-28A(+) / Details (production host): Novagen / Production host: ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 674 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / ![]() #3: Chemical | ![]() #4: Chemical | ChemComp-EDO / ![]() #5: Chemical | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.86 Å3/Da / Density % sol: 68.16 % |
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Crystal grow![]() | Temperature: 295 K / Method: microbatch / pH: 7.5 Details: 10-15% PEG 400, 1.25M Ammonium sulphate, 100mM HEPES sodium salt |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 2, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→24.58 Å / Num. obs: 97939 / % possible obs: 99.9 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.993 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 14187 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2GEU Resolution: 1.8→24.58 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.324 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.587 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→24.58 Å
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