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- PDB-3aez: Pantothenate kinase from Mycobacterium tuberculosis (MtPanK) in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3aez | ||||||
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Title | Pantothenate kinase from Mycobacterium tuberculosis (MtPanK) in complex with GDP and Phosphopantothenate | ||||||
![]() | Pantothenate kinase | ||||||
![]() | TRANSFERASE / Homodimer / COA biosynthesis / Nucleotide binding / ATP-binding / Kinase / Nucleotide-binding | ||||||
Function / homology | ![]() pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Chetnani, B. / Kumar, P. / Surolia, A. / Vijayan, M. | ||||||
![]() | ![]() Title: M. tuberculosis pantothenate kinase: dual substrate specificity and unusual changes in ligand locations Authors: Chetnani, B. / Kumar, P. / 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 | ![]() | 87.6 KB | Display | ![]() |
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PDB format | ![]() | 64.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3af0C ![]() 3af1C ![]() 3af2C ![]() 3af3C ![]() 3af4C ![]() 2gevS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 35704.848 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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-Non-polymers , 5 types, 279 molecules ![](data/chem/img/GDP.gif)
![](data/chem/img/PAZ.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PAZ.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GDP / | ||||
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#3: Chemical | ChemComp-PAZ / | ||||
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.93 Å3/Da / Density % sol: 68.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.4-1.8M tri sodium citrate, 0.05-0.1M sodium acetate, 10% glycerol, pH 6.5, 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: Apr 24, 2009 / Details: Mirrors |
Radiation | Monochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. obs: 28891 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 51.1 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4159 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2GEV Resolution: 2.2→34.06 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.018 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.597 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→34.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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