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- PDB-3nnt: Crystal Structure of K170M Mutant of Type I 3-Dehydroquinate Dehy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3nnt | ||||||
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Title | Crystal Structure of K170M Mutant of Type I 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2 in Non-Covalent Complex with Dehydroquinate. | ||||||
![]() | 3-dehydroquinate dehydratase | ||||||
![]() | LYASE / Structural Genomics / 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.1 KB | Display | ![]() |
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PDB format | ![]() | 98.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3js3C ![]() 3m7wC ![]() 3lb0S 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: 30103.324 Da / Num. of mol.: 2 / Mutation: K170M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: LT2 / Gene: aroD, STM1358 / Plasmid: pMCSG7 / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.26 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 3 Details: Protein solution: 7.5 mG/mL, 0.25M Sodium chloride, 0.01M Tris pH 8.3, 2mM 3-Dehydroquinic acid (DHR); Screen solution: Classics F9, 0.05M Potassium phosphate, 20%(w/v) PEG 8000., VAPOR ...Details: Protein solution: 7.5 mG/mL, 0.25M Sodium chloride, 0.01M Tris pH 8.3, 2mM 3-Dehydroquinic acid (DHR); Screen solution: Classics F9, 0.05M Potassium phosphate, 20%(w/v) PEG 8000., 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: Jun 18, 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: 1.6→30 Å / Num. all: 58590 / Num. obs: 58590 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 2 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2.25 / Num. unique all: 2852 / % possible all: 95 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3LB0 Resolution: 1.6→29.65 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.754 / SU ML: 0.061 Isotropic thermal model: Atomic thermal factors individually refined Cross valid method: THROUGHOUT / ESU R Free: 0.09 / 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: 19.535 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→29.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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