+Open data
-Basic information
Entry | Database: PDB / ID: 6dfe | |||||||||
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Title | The structure of a ternary complex of E. coli WaaC | |||||||||
Components | ADP-heptose--LPS heptosyltransferase | |||||||||
Keywords | TRANSFERASE / llipopolysaccharide heptosyltransferase | |||||||||
Function / homology | Function and homology information lipopolysaccharide heptosyltransferase activity / Transferases / lipopolysaccharide core region biosynthetic process Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | |||||||||
Authors | Worrall, L.J. / Blaukopf, M. / Withers, S.G. / Strynadka, N.C.J. | |||||||||
Citation | Journal: Structure / Year: 2018 Title: Insights into Heptosyltransferase I Catalysis and Inhibition through the Structure of Its Ternary Complex. Authors: Blaukopf, M. / Worrall, L. / Kosma, P. / Strynadka, N.C.J. / Withers, S.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dfe.cif.gz | 145.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dfe.ent.gz | 111.8 KB | Display | PDB format |
PDBx/mmJSON format | 6dfe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/6dfe ftp://data.pdbj.org/pub/pdb/validation_reports/df/6dfe | HTTPS FTP |
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-Related structure data
Related structure data | 2h1hS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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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: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: 1 - 321 / Label seq-ID: 1 - 321
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-Components
#1: Protein | Mass: 36242.449 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: AL530_003015, AZZ83_001895, C1N95_02680, CT143_12860, CT146_13830, WM48_19965 Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A152KUZ3 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.45 Å3/Da / Density % sol: 49.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM Hepes (pH 7.0), 15% (w/v) PEG 1500, 100 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00001 Å | ||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.31→40.09 Å / Num. obs: 31688 / % possible obs: 99.5 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.029 / Rrim(I) all: 0.079 / Net I/σ(I): 17.8 / Num. measured all: 223845 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2h1h Resolution: 2.31→40.09 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.758 / SU ML: 0.202 / SU R Cruickshank DPI: 0.3792 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.379 / ESU R Free: 0.244 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: 137.77 Å2 / Biso mean: 46.925 Å2 / Biso min: 22.54 Å2
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Refinement step | Cycle: final / Resolution: 2.31→40.09 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 20564 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.31→2.37 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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