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- PDB-2iyq: Shikimate kinase from Mycobacterium tuberculosis in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2iyq | ||||||
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Title | Shikimate kinase from Mycobacterium tuberculosis in complex with shikimate and ADP | ||||||
![]() | SHIKIMATE KINASE![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hartmann, M.D. / Bourenkov, G.P. / Oberschall, A. / Strizhov, N. / Bartunik, H.D. | ||||||
![]() | ![]() Title: Mechanism of Phosphoryl Transfer Catalyzed by Shikimate Kinase from Mycobacterium Tuberculosis. Authors: Hartmann, M.D. / Bourenkov, G.P. / Oberschall, A. / Strizhov, N. / Bartunik, H.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.9 KB | Display | ![]() |
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PDB format | ![]() | 36.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2iyrC ![]() 2iysC ![]() 2iytC ![]() 2iyuC ![]() 2iyvC ![]() 2iywC ![]() 2iyxC ![]() 2iyyC ![]() 2iyzC ![]() 1u8aS 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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | ![]() Mass: 19683.506 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P0A4Z2, UniProt: P9WPY3*PLUS, ![]() |
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-Non-polymers , 5 types, 153 molecules ![](data/chem/img/SKM.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SKM / (![]() | ||
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#3: Chemical | ChemComp-ADP / ![]() | ||
#4: Chemical | ChemComp-TRS / ![]() | ||
#5: Chemical | ChemComp-CL / ![]() #6: Water | ChemComp-HOH / | ![]() |
-Details
Sequence details | C-TERMINAL HIS-TAG |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53.1 % |
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Crystal grow![]() | pH: 8.6 Details: 250MM LICL, 20%(W/V) PEG 2000, 100MM TRIS-HCL PH 8.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 25, 2005 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→19.1 Å / Num. obs: 20228 / % possible obs: 97 % / Redundancy: 3.08 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.62 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 3 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.63 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1U8A Resolution: 1.8→19.1 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.003 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.29 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.1 Å
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Refine LS restraints |
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