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- PDB-5ypq: Crystal structure of sulfated dehydroquinate dehydratase from Aci... -
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Basic information
Entry | Database: PDB / ID: 5ypq | ||||||
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Title | Crystal structure of sulfated dehydroquinate dehydratase from Acinetobacter baumannii at 2.65 A resolution | ||||||
![]() | 3-dehydroquinate dehydratase | ||||||
![]() | 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. | ||||||
![]() | ![]() Title: Crystal structure of sulfated dehydroquinate dehydratase from Acinetobacter baumannii at 2.65 A resolution Authors: Iqbal, N. / Kaur, P. / Sharma, S. / Singh, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 340.2 KB | Display | ![]() |
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PDB format | ![]() | 279.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 540.1 KB | Display | ![]() |
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Full document | ![]() | 558.1 KB | Display | |
Data in XML | ![]() | 62.5 KB | Display | |
Data in CIF | ![]() | 85.2 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: 16516.803 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377 Gene: aroQ, A1S_2009 / Production host: ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.5M Ammonium Sulfate, 0.1M tris pH 8.5, 12% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 3, 2017 / Details: MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 2.647→109.948 Å / Num. obs: 58629 / % possible obs: 98.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.647→2.693 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2866 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5B6P Resolution: 2.65→109.95 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.904 / SU B: 13.805 / SU ML: 0.282 / Cross valid method: THROUGHOUT / ESU R Free: 0.342 / 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: 49.889 Å2
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Refinement step | Cycle: 1 / Resolution: 2.65→109.95 Å
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Refine LS restraints |
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