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- PDB-2zs9: Pantothenate kinase from Mycobacterium tuberculosis (MtPanK) in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zs9 | ||||||
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Title | Pantothenate kinase from Mycobacterium tuberculosis (MtPanK) in complex with ADP and Pantothenate | ||||||
![]() | Pantothenate kinase | ||||||
![]() | TRANSFERASE / homodimer / COA biosynthesis / nucleotide binding / ATP-binding / Coenzyme A biosynthesis / Kinase | ||||||
Function / homology | ![]() pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / phosphorylation / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Chetnani, B. / Das, S. / Kumar, P. / Surolia, A. / Vijayan, M. | ||||||
![]() | ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.2 KB | Display | ![]() |
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PDB format | ![]() | 57.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 807.5 KB | Display | ![]() |
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Full document | ![]() | 817.5 KB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zs7C ![]() 2zs8C ![]() 2zsaC ![]() 2zsbC ![]() 2zsdC ![]() 2zseC ![]() 2zsfC ![]() 2gevS 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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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, 197 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PAU.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PAU.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ADP / | ||||||
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#3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | ChemComp-PAU / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.96 Å3/Da / Density % sol: 68.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.4M to 1.8M tri sodium citrate, 0.05M-0.1M sodium acetate, 7.5%-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: May 16, 2006 / 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: 2.7→40 Å / Num. obs: 15934 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 71.7 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 34.2 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 4.7 / Num. unique all: 1554 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2GEV Resolution: 2.7→34.12 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1480370.64 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 72.4604 Å2 / ksol: 0.405514 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→34.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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