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Yorodumi- PDB-6sfe: CRYSTAL STRUCTURE OF DHQ1 FROM SALMONELLA TYPHI COVALENTLY MODIFI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sfe | ||||||
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Title | CRYSTAL STRUCTURE OF DHQ1 FROM SALMONELLA TYPHI COVALENTLY MODIFIED BY COMPOUND 7 | ||||||
Components | 3-dehydroquinate dehydratase | ||||||
Keywords | LYASE / LYASE ACTIVITY / CHORISMATE BIOSYNTHETIC PROCESS / 3-DEHYDROQUINASE / COVALENT INHIBITOR | ||||||
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 typhi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å | ||||||
Authors | Sanz-Gaitero, M. / Lence, E. / Maneiro, M. / Thompson, R. / Hawkins, A.R. / Gonzalez-Bello, C. / van Raaij, M.J. | ||||||
Funding support | Spain, 1items
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Citation | 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sfe.cif.gz | 245.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sfe.ent.gz | 197.2 KB | Display | PDB format |
PDBx/mmJSON format | 6sfe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sf/6sfe ftp://data.pdbj.org/pub/pdb/validation_reports/sf/6sfe | HTTPS FTP |
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-Related structure data
Related structure data | 6sfgC 6sfhC 4uioS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / 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: 0 / 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.) Salmonella typhi (bacteria) / Gene: aroD, STY1760, t1231 / Production host: Escherichia coli (E. coli) / References: UniProt: P24670, 3-dehydroquinate dehydratase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 30% PEG 2000 MME, 100mM HEPES pH7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å | ||||||||||||||||||||||||
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: 1.08→51.03 Å / Num. obs: 187841 / % possible obs: 98.1 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.043 / Rrim(I) all: 0.08 / Net I/σ(I): 12.4 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4UIO Resolution: 1.08→51.03 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.735 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.026 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 66.98 Å2 / Biso mean: 9.045 Å2 / Biso min: 1.64 Å2
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Refinement step | Cycle: final / Resolution: 1.08→51.03 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 16334 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.08→1.104 Å / Rfactor Rfree error: 0
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