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- PDB-3o1n: 1.03 Angstrom Crystal Structure of Q236A Mutant Type I Dehydroqui... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3o1n | ||||||
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Title | 1.03 Angstrom Crystal Structure of Q236A Mutant Type I Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium | ||||||
![]() | 3-dehydroquinate dehydratase | ||||||
![]() | LYASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / TIM barrel / dehydratase | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Light, S.H. / Minasov, G. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: A conserved surface loop in type I dehydroquinate dehydratases positions an active site arginine and functions in substrate binding. Authors: Light, S.H. / Minasov, G. / Shuvalova, L. / Peterson, S.N. / Caffrey, M. / Anderson, W.F. / Lavie, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 249.4 KB | Display | ![]() |
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PDB format | ![]() | 201.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 439.2 KB | Display | ![]() |
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Full document | ![]() | 442.4 KB | Display | |
Data in XML | ![]() | 28.4 KB | Display | |
Data in CIF | ![]() | 45.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3l2iSC ![]() 3oexC 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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Unit cell |
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Components
#1: Protein | Mass: 30044.258 Da / Num. of mol.: 2 / Mutation: Q236A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: LT2 / Gene: aroD, STM1358 / Plasmid: pMCSG7 / Production host: ![]() ![]() #2: Chemical | ChemComp-CL / | #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.49 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Protein: 7.5 mg/mL, 0.5M Sodium Chloride, 0.01M Tris-HCL (pH 8.3); Screen: Classics II (H1), 0.2M Magnesium chloride, 0.1M Tris, pH 8.5, 25% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 22, 2010 / Details: Beryllium lenses |
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.03→30 Å / Num. all: 196964 / Num. obs: 196964 / % possible obs: 92.7 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.03→1.05 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 3.7 / Num. unique all: 8952 / % possible all: 84.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3L2I Resolution: 1.03→26.62 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.763 / SU ML: 0.018 Isotropic thermal model: Anisotropically refined individual B-factors Cross valid method: THROUGHOUT / ESU R Free: 0.028 / 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: 10.933 Å2
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Refinement step | Cycle: LAST / Resolution: 1.03→26.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.03→1.057 Å / Total num. of bins used: 20
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