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- PDB-2gev: Pantothenate kinase from Mycobacterium tuberculosis (MtPanK) in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2gev | ||||||
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Title | Pantothenate kinase from Mycobacterium tuberculosis (MtPanK) in complex with a coenzyme A derivative, Form-II (LT) | ||||||
![]() | Pantothenate kinase | ||||||
![]() | TRANSFERASE / HOMODIMER / COA BIOSYNTHESIS / NUCLEOTIDE BINDING | ||||||
Function / homology | ![]() pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Das, S. / Kumar, P. / Bhor, V. / Surolia, A. / Vijayan, M. | ||||||
![]() | ![]() 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. #1: Journal: ACTA CRYSTALLOGR.,SECT.F / 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.4 KB | Display | ![]() |
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PDB format | ![]() | 64.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2gesC ![]() 2getC ![]() 2geuC ![]() 1esmS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | The following symmetry operation will generate the second subunit of the homodimeric MtPanK molecule: Symmetry:Y, X, -Z; TransSymm: 556 |
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Components
#1: Protein | Mass: 35780.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P63810, UniProt: P9WPA7*PLUS, pantothenate kinase | ||
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#2: Chemical | ChemComp-COK / [( | ||
#3: Chemical | ChemComp-TRS / | ||
#4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.9 Å3/Da / Density % sol: 68.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10-15%(w/v) PEG8000, 0.05M NaCl, 0.05-0.1M NaOAc in 0.1M Na-Cacodylate buffer of pH 6.5, 0.001M Beta-mercaptoethanol was present in the protein buffer, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 3, 2005 |
Radiation | Monochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→28.64 Å / Num. obs: 24164 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 15 % / Biso Wilson estimate: 47.7 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 10 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 4.1 / Num. unique all: 2374 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ID 1ESM Resolution: 2.35→28.64 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1252803.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: MLF FUNCTION THROUGHOUT THE REFINEMENT
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.7104 Å2 / ksol: 0.321857 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→28.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.43 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 10
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Xplor file |
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