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- PDB-4ly0: Crystal structure WlaRD, a sugar 3N-formyl transferase in the pre... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ly0 | ||||||
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Title | Crystal structure WlaRD, a sugar 3N-formyl transferase in the presence of dTDP-Glc and 10-N-Formyl-THF | ||||||
![]() | WlaRD, a sugar 3N-formyl transferase | ||||||
![]() | TRANSFERASE / formyltransferase / formylation | ||||||
Function / homology | Rossmann fold - #12230 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Chem-1YA / 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE / : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Thoden, J.B. / Goneau, M.-F. / Gilbert, M. / Holden, H.M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 150.8 KB | Display | ![]() |
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PDB format | ![]() | 116.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 32.8 KB | Display | |
Data in CIF | ![]() | 50 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4lxqSC ![]() 4lxtC ![]() 4lxuC ![]() 4lxxC ![]() 4lxyC ![]() 4ly3C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Strain: 81116 / Gene: C8J_1081 / Plasmid: pET28 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 804 molecules ![](data/chem/img/1YA.gif)
![](data/chem/img/DAU.gif)
![](data/chem/img/MPO.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DAU.gif)
![](data/chem/img/MPO.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.52 % |
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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 N5-formyl-THF, 5 mM TDP, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: May 1, 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: 1.6→50 Å / Num. all: 96212 / Num. obs: 96212 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2.2 / Num. unique all: 13596 / Rsym value: 0.305 / % possible all: 79.1 |
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Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4LXQ Resolution: 1.6→45.72 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.708 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.085 / 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: 17.121 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→45.72 Å
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Refine LS restraints |
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