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- PDB-2iyu: Shikimate kinase from Mycobacterium tuberculosis in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2iyu | ||||||
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Title | Shikimate kinase from Mycobacterium tuberculosis in complex with ADP, open LID (conf. A) | ||||||
![]() | SHIKIMATE KINASE | ||||||
![]() | TRANSFERASE / AROMATIC AMINO ACID BIOSYNTHESIS / P-LOOP KINASE / METAL- BINDING / SHIKIMATE KINASE / SHIKIMATE PATHWAY / NUCLEOTIDE- BINDING / AMINO-ACID BIOSYNTHESIS / KINASE / MAGNESIUM / ATP-BINDING | ||||||
Function / homology | ![]() shikimate kinase / shikimate metabolic process / Chorismate via Shikimate Pathway / shikimate kinase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / phosphorylation / magnesium ion binding / ATP binding / cytosol 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 | ![]() | 51 KB | Display | ![]() |
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PDB format | ![]() | 35.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 779.2 KB | Display | ![]() |
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Full document | ![]() | 780.8 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Data in CIF | ![]() | 15.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2iyqC ![]() 2iyrC ![]() 2iysSC ![]() 2iytC ![]() 2iyvC ![]() 2iywC ![]() 2iyxC ![]() 2iyyC ![]() 2iyzC 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
#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, shikimate kinase |
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#2: Chemical | ChemComp-ADP / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
Sequence details | C-TERMINAL HIS-TAG |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 30.3 % |
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Crystal grow | pH: 8.5 Details: 170MM NA ACETATE, 15%(V/V) GLYCEROL, 25.5%(W/V) PEG 4000, 85MM TRIS-HCL PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 24, 2005 / Details: MORRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→19.81 Å / Num. obs: 13255 / % possible obs: 98 % / Redundancy: 4.67 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.38 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.05 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2IYS Resolution: 1.85→19.81 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.859 / SU B: 4.544 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.192 / 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: 26.35 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→19.81 Å
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Refine LS restraints |
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