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- PDB-6h5c: Crystal structure of DHQ1 from Salmonella typhi covalently modifi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6h5c | ||||||
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Title | Crystal structure of DHQ1 from Salmonella typhi covalently modified by ligand 1 | ||||||
![]() | 3-dehydroquinate dehydratase | ||||||
![]() | LYASE / lyase activity / chorismate biosynthetic process / 3-dehydroquinase / covalent inhibitor | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Sanz-Gaitero, M. / Maneiro, M. / Lence, E. / Otero, J.M. / Thompson, P. / Hawkins, A.R. / Gonzalez-Bello, C. / van Raaij, M.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Hydroxylammonium Derivatives for Selective Active-site Lysine Modification in the Anti-virulence Bacterial Target DHQ1 Enzyme. Authors: Maneiro, M. / Lence, E. / Sanz-Gaitero, M. / Otero, J.M. / van Raaij, M.J. / Thompson, P. / Hawkins, A.R. / Gonzalez-Bello, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 235.8 KB | Display | ![]() |
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PDB format | ![]() | 190.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.7 KB | Display | ![]() |
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Full document | ![]() | 443.9 KB | Display | |
Data in XML | ![]() | 26.4 KB | Display | |
Data in CIF | ![]() | 41.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6h5dC ![]() 6h5gC ![]() 6h5jC ![]() 4uioS S: Starting model for refinement C: citing same article ( |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 1 - 252 / Label seq-ID: 1 - 252
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Components
#1: Protein | Mass: 27680.992 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: aroD, STY1760, t1231 / 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: 2.16 Å3/Da / Density % sol: 43.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 24% PEG 2000 MME, 100 mM HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.14→38.14 Å / Num. obs: 150270 / % possible obs: 88.6 % / Redundancy: 1.8 % / Biso Wilson estimate: 12.4 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.071 / Rrim(I) all: 0.101 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 1.14→1.2 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 21721 / CC1/2: 0.61 / Rpim(I) all: 0.67 / Rrim(I) all: 0.948 / % possible all: 87.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4UIO Resolution: 1.14→38.14 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.804 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.04 / 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: 13.783 Å2
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Refinement step | Cycle: 1 / Resolution: 1.14→38.14 Å
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Refine LS restraints |
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