+Open data
-Basic information
Entry | Database: PDB / ID: 5wxi | |||||||||
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Title | EarP bound with dTDP-rhamnose (soaked) | |||||||||
Components | EarP | |||||||||
Keywords | TRANSFERASE / glycosyltransferase / GT-B / EF-P / rhamnosylation / translation elongation / dTDP-rhamnose | |||||||||
Function / homology | protein-arginine rhamnosyltransferase activity / Protein-arginine rhamnosyltransferase EarP / Elongation-Factor P (EF-P) rhamnosyltransferase EarP / Transferases; Glycosyltransferases; Hexosyltransferases / BETA-MERCAPTOETHANOL / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE / Protein-arginine rhamnosyltransferase Function and homology information | |||||||||
Biological species | Neisseria meningitidis serogroup B / serotype 15 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | |||||||||
Authors | Sengoku, T. / Yokoyama, S. / Yanagisawa, T. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Nat. Chem. Biol. / Year: 2018 Title: Structural basis of protein arginine rhamnosylation by glycosyltransferase EarP Authors: Sengoku, T. / Suzuki, T. / Dohmae, N. / Watanabe, C. / Honma, T. / Hikida, Y. / Yamaguchi, Y. / Takahashi, H. / Yokoyama, S. / Yanagisawa, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wxi.cif.gz | 333.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wxi.ent.gz | 270.4 KB | Display | PDB format |
PDBx/mmJSON format | 5wxi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wxi_validation.pdf.gz | 998.8 KB | Display | wwPDB validaton report |
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Full document | 5wxi_full_validation.pdf.gz | 1006.1 KB | Display | |
Data in XML | 5wxi_validation.xml.gz | 36 KB | Display | |
Data in CIF | 5wxi_validation.cif.gz | 53.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/5wxi ftp://data.pdbj.org/pub/pdb/validation_reports/wx/5wxi | HTTPS FTP |
-Related 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: 44219.992 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis serogroup B / serotype 15 (strain H44/76) (bacteria) Strain: H44/76 / Gene: NMH_0797 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / References: UniProt: E6MVV9 |
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-Non-polymers , 5 types, 651 molecules
#2: Chemical | #3: Chemical | ChemComp-BME / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / | #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: 2.5 Å3/Da / Density % sol: 50.78 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1M Hepes-NaOH buffer (pH 6.8-7.5), 20% PEG3350, 0.2M ammonium sulfate PH range: 6.8-7.5 |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→48.85 Å / Num. obs: 61063 / % possible obs: 100 % / Redundancy: 7.3 % / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1.9 / CC1/2: 0.649 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: apo EarP Resolution: 2→48.847 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.11
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→48.847 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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