+Open data
-Basic information
Entry | Database: PDB / ID: 2h1f | ||||||
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Title | E. coli heptosyltransferase WaaC with ADP | ||||||
Components | Lipopolysaccharide heptosyltransferase-1 | ||||||
Keywords | TRANSFERASE / Gt-B fold absence of C-terminal alpha-helix | ||||||
Function / homology | Function and homology information lipopolysaccharide heptosyltransferase activity / Transferases / lipopolysaccharide core region biosynthetic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Escherichia coli O6 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Grizot, S. / Salem, M. / Vongsouthi, V. / Durand, L. / Moreau, F. / Dohi, H. / Vincent, S. / Escaich, S. / Ducruix, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Structure of the Escherichia coli heptosyltransferase WaaC: binary complexes with ADP and ADP-2-deoxy-2-fluoro heptose. Authors: Grizot, S. / Salem, M. / Vongsouthi, V. / Durand, L. / Moreau, F. / Dohi, H. / Vincent, S. / Escaich, S. / Ducruix, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h1f.cif.gz | 134 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h1f.ent.gz | 104.5 KB | Display | PDB format |
PDBx/mmJSON format | 2h1f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/2h1f ftp://data.pdbj.org/pub/pdb/validation_reports/h1/2h1f | HTTPS FTP |
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-Related structure data
Related structure data | 2gt1SC 2h1hC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37345.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O6 (bacteria) / Species: Escherichia coli / Strain: RS218 / Gene: rfaC / Plasmid: pET-30b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q8FC98, UniProt: A0A0H2VC26*PLUS, Transferases #2: Chemical | #3: 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: 2.17 Å3/Da / Density % sol: 43.25 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7 Details: 15% PEG 1500, 100 mM Hepes (pH 7.0), 100 mM NaCl, 1 mM ADP, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9795 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 28, 2004 / Details: curvated mirrors |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→33.5 Å / Num. all: 25250 / Num. obs: 25122 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rsym value: 0.056 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 1623 / Rsym value: 0.259 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Native WaaC PDB ENTRY 2GT1 Resolution: 2.4→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 21.387 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.943 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.51 Å /
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Xplor file |
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