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Open data
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Basic information
Entry | Database: PDB / ID: 5xmb | ||||||
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Title | Mycobacterium tuberculosis Pantothenate kinase mutant F247A | ||||||
![]() | Pantothenate kinase | ||||||
![]() | TRANSFERASE / Homodimer / CoA biosynthesis / Nucleotide binding / Concerted movement / Structural transformation | ||||||
Function / homology | ![]() pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / phosphorylation / ATP binding / plasma membrane / cytoplasm 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 | ![]() | 215.7 KB | Display | ![]() |
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PDB format | ![]() | 168.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 477.3 KB | Display | ![]() |
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Full document | ![]() | 493.6 KB | Display | |
Data in XML | ![]() | 38.2 KB | Display | |
Data in CIF | ![]() | 51.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xlvC ![]() 5xlwC ![]() 2geuS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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Components
#1: Protein | Mass: 35628.754 Da / Num. of mol.: 4 / Mutation: F247A 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: ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.69 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 5.5 Details: 25%PEG 3350, 200mM Ammonium sulphate, 100mM Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953725 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→84.96 Å / Num. obs: 20268 / % possible obs: 89.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.249 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 4 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2961 / % possible all: 93.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2GEU Resolution: 3.2→84.96 Å / Cor.coef. Fo:Fc: 0.82 / Cor.coef. Fo:Fc free: 0.71 / SU B: 49.442 / SU ML: 0.839 / Cross valid method: THROUGHOUT / ESU R Free: 0.795 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.349 Å2
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Refinement step | Cycle: 1 / Resolution: 3.2→84.96 Å
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Refine LS restraints |
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