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- PDB-5yhm: Crystal structure of dehydroquinate dehydratase with tris induced... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5yhm | ||||||
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Title | Crystal structure of dehydroquinate dehydratase with tris induced oligomerisation at 1.907 Angstrom resolution | ||||||
![]() | (3-dehydroquinate dehydratase) x 2 | ||||||
![]() | LYASE | ||||||
Function / homology | ![]() quinate catabolic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Iqbal, N. / Kaur, P. / Sharma, S. / Singh, T.P. | ||||||
![]() | ![]() Title: Crystal structure of dehydroquinate dehydratase with tris induced oligomerisation at 1.907 Angstrom resolution Authors: Iqbal, N. / Kaur, P. / Sharma, S. / Singh, T.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 346.5 KB | Display | ![]() |
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PDB format | ![]() | 283.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 551 KB | Display | ![]() |
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Full document | ![]() | 578.1 KB | Display | |
Data in XML | ![]() | 65.2 KB | Display | |
Data in CIF | ![]() | 90.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5b6pS 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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Unit cell |
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Components
#1: Protein | Mass: 15886.130 Da / Num. of mol.: 11 / Fragment: UNP residues 3-147 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 17978 / NCDC KC 755 / Gene: aroQ, A1S_2009 / Production host: ![]() ![]() #2: Protein | | Mass: 16104.404 Da / Num. of mol.: 1 / Fragment: UNP residues 1-147 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 17978 / NCDC KC 755 / Gene: aroQ, A1S_2009 / Production host: ![]() ![]() #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-TRS / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1.5M Ammonium sulphate, 0.1M tris, 12% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→45.7 Å / Num. obs: 139447 / % possible obs: 89.8 % / Redundancy: 3.2 % / Rpim(I) all: 0.134 / Net I/σ(I): 5.96 |
Reflection shell | Resolution: 1.91→1.956 Å / Num. unique obs: 1715 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5B6P Resolution: 1.91→45.7 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.976 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.157 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.754 Å2
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Refinement step | Cycle: 1 / Resolution: 1.91→45.7 Å
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Refine LS restraints |
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