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Yorodumi- PDB-8b2c: Crystal structure of type I dehydroquinase from Salmonella typhi ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8b2c | |||||||||
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Title | Crystal structure of type I dehydroquinase from Salmonella typhi inhibited by an epoxide derivative | |||||||||
Components | 3-dehydroquinate dehydratase | |||||||||
Keywords | LYASE / CHORISMATE BIOSYNTHETIC PROCESS / 3-DEHYDROQUINASE | |||||||||
Function / homology | Function and homology information 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 | Salmonella enterica subsp. enterica serovar Typhi (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | |||||||||
Authors | Otero, J.M. / Rodriguez, A. / Maneiro, M. / Lence, E. / Thompson, P. / Hawkins, A.R. / Gonzalez-Bello, C. / van Raaij, M.J. | |||||||||
Funding support | Spain, 2items
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Citation | Journal: Front Mol Biosci / Year: 2023 Title: Quinate-based ligands for irreversible inactivation of the bacterial virulence factor DHQ1 enzyme-A molecular insight. Authors: Rodriguez, A. / Maneiro, M. / Lence, E. / Otero, J.M. / van Raaij, M.J. / Thompson, P. / Hawkins, A.R. / Gonzalez-Bello, C. #1: Journal: Chemistry / Year: 2020 Title: Self-Immolation of a Bacterial Dehydratase Enzyme by its Epoxide Product. Authors: Lence, E. / Maneiro, M. / Sanz-Gaitero, M. / van Raaij, M.J. / Thompson, P. / Hawkins, A.R. / Gonzalez-Bello, C. #2: Journal: Organic Chemistry Frontiers / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b2c.cif.gz | 69.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b2c.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8b2c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/8b2c ftp://data.pdbj.org/pub/pdb/validation_reports/b2/8b2c | HTTPS FTP |
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-Related structure data
Related structure data | 8b2aC 8b2bC 4cnnS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27680.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi (bacteria) Gene: aroD, STY1760, t1231 / Production host: Escherichia coli (E. coli) / References: UniProt: P24670, 3-dehydroquinate dehydratase | ||||
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#2: Chemical | ChemComp-OVU / ( | ||||
#3: Chemical | ChemComp-EPE / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 36 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 26 % (w/v) PEG 2000 MME, 0.1 M HEPES-NaOH |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.00556 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00556 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→105.2 Å / Num. obs: 28123 / % possible obs: 89.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 13.361 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.019 / Rrim(I) all: 0.041 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.55→1.63 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 3317 / CC1/2: 0.903 / Rpim(I) all: 0.209 / Rrim(I) all: 0.452 / % possible all: 73.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4CNN Resolution: 1.55→52.6 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.666 / SU ML: 0.06 / Cross valid method: FREE R-VALUE / ESU R: 0.094 / ESU R Free: 0.093 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.196 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→52.6 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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