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- PDB-3hr7: Crystal structure of the shikimate kinase-sulfate complex from He... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3hr7 | ||||||
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Title | Crystal structure of the shikimate kinase-sulfate complex from Helicobacter pylori | ||||||
![]() | Shikimate kinase | ||||||
![]() | TRANSFERASE / three-layer alpha/beta fold / nucleoside monophosphate (NMP) kinase family / Amino-acid biosynthesis / Aromatic amino acid biosynthesis / ATP-binding / Kinase / Magnesium / Metal-binding / Nucleotide-binding | ||||||
Function / homology | ![]() shikimate kinase / 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 | ![]() ![]() ![]() | ||||||
![]() | Cheng, W.C. / Wang, W.C. | ||||||
![]() | ![]() Title: Structures of Helicobacter pylori shikimate kinase reveal a selective inhibitor-induced-fit mechanism Authors: Cheng, W.C. / Chen, Y.F. / Wang, H.J. / Hsu, K.C. / Lin, S.C. / Chen, T.J. / Yang, J.M. / Wang, W.C. #1: ![]() Title: Structural basis for shikimate-binding specificity of Helicobacter pylori shikimate kinase Authors: Cheng, W.C. / Chang, Y.N. / Wang, W.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.8 KB | Display | ![]() |
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PDB format | ![]() | 59.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.6 KB | Display | ![]() |
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Full document | ![]() | 453.4 KB | Display | |
Data in XML | ![]() | 16.8 KB | Display | |
Data in CIF | ![]() | 24.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3mrsC ![]() 3mufC ![]() 3n2eC ![]() 1zuhS 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
#1: Protein | Mass: 19265.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 30% PEG 8000, 0.2M lithium sulphate, 0.1M sodium acetate buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 10, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→74.33 Å / Num. obs: 49284 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.068 |
Reflection shell | Highest resolution: 1.8 Å / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ZUH Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.919 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.117 / ESU R Free: 0.117 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.453 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.804→1.851 Å / Total num. of bins used: 20
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