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- PDB-3m7w: Crystal Structure of Type I 3-Dehydroquinate Dehydratase (aroD) f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3m7w | ||||||
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Title | Crystal Structure of Type I 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2 in Covalent Complex with Dehydroquinate | ||||||
![]() | 3-dehydroquinate dehydratase | ||||||
![]() | LYASE / Type I 3-Dehydroquinase / DHQase_I / Dehydroquinate / idp90922 / Amino-acid biosynthesis / Aromatic amino acid biosynthesis / Schiff base / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | ![]() 3,4-dihydroxybenzoate biosynthetic 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 | ![]() ![]() ![]() | ||||||
![]() | Minasov, G. / Light, S.H. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: Insights into the mechanism of type I dehydroquinate dehydratases from structures of reaction intermediates. Authors: Light, S.H. / Minasov, G. / Shuvalova, L. / Duban, M.E. / Caffrey, M. / Anderson, W.F. / Lavie, A. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 319.6 KB | Display | ![]() |
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PDB format | ![]() | 259.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 496.2 KB | Display | ![]() |
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Full document | ![]() | 507.4 KB | Display | |
Data in XML | ![]() | 66.9 KB | Display | |
Data in CIF | ![]() | 94 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3js3C ![]() 3nntC ![]() 3l2iS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27629.652 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: LT2 / Gene: aroD, STM1358 / Plasmid: pMCSG7 / Production host: ![]() ![]() #2: Chemical | ChemComp-DQA / #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: 2.07 Å3/Da / Density % sol: 40.69 % |
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Crystal grow | Temperature: 295 K / pH: 4.6 Details: Protein solution: 7.5 mg/mL, 0.5M Sodium Chloride, 0.01M Tris-HCL (pH 8.3); Screen solution: ANL-2 (E7), 0.17M Ammonium acetate, 0.085M Sodium acetate (pH 4.6), 25.5% PEG 4000, 15% Glycerol; ...Details: Protein solution: 7.5 mg/mL, 0.5M Sodium Chloride, 0.01M Tris-HCL (pH 8.3); Screen solution: ANL-2 (E7), 0.17M Ammonium acetate, 0.085M Sodium acetate (pH 4.6), 25.5% PEG 4000, 15% Glycerol; Soak: 5mM Dehydroquinic acid in screen solution for 20 min., VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 8, 2010 / Details: BERYLLIUM LENSES |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. obs: 99121 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3L2I Resolution: 1.95→29.69 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.393 / SU ML: 0.098 / Isotropic thermal model: Refined individually / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.151 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.01 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→29.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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