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Yorodumi- PDB-4ly3: Crystal structure of WlaRD, a sugar 3N-formyl transferase in the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ly3 | ||||||
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Title | Crystal structure of WlaRD, a sugar 3N-formyl transferase in the presence of dTPD-Qui3N, dTDP-Qui3NFo, and THF | ||||||
Components | WlaRD a sugar 3N formyltransferase | ||||||
Keywords | TRANSFERASE / formyltransferase | ||||||
Function / homology | Rossmann fold - #12230 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / : / Chem-1YJ / Chem-T3Q / : Function and homology information | ||||||
Biological species | Campylobacter jejuni subsp. jejuni (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Thoden, J.B. / Goneau, M.-F. / Gilbert, M. / Holden, H.M. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Structure of a sugar N-formyltransferase from Campylobacter jejuni. Authors: Thoden, J.B. / Goneau, M.F. / Gilbert, M. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ly3.cif.gz | 143.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ly3.ent.gz | 110.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ly3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ly3_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4ly3_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4ly3_validation.xml.gz | 29.4 KB | Display | |
Data in CIF | 4ly3_validation.cif.gz | 44.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/4ly3 ftp://data.pdbj.org/pub/pdb/validation_reports/ly/4ly3 | HTTPS FTP |
-Related structure data
Related structure data | 4lxqSC 4lxtC 4lxuC 4lxxC 4lxyC 4ly0C 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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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 31936.607 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter) Strain: 81116 / Gene: C8J_1081 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: A8FMJ3 |
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-Non-polymers , 5 types, 615 molecules
#2: Chemical | #3: Chemical | ChemComp-T3Q / [( | #4: Chemical | #5: Chemical | ChemComp-1YF / [( | #6: 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: 3.12 Å3/Da / Density % sol: 60.53 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 11-15% PEG 8000, 200 mM NaCl, 5 mM TDP, 5 mM N-5-formyl-THF, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: May 20, 2013 / Details: mirrors |
Radiation | Monochromator: montel optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 58443 / Num. obs: 58443 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 15.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 4LXQ Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.258 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.94 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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