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Yorodumi- PDB-5nv8: Structural basis for EarP-mediated arginine glycosylation of tran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nv8 | ||||||
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Title | Structural basis for EarP-mediated arginine glycosylation of translation elongation factor EF-P | ||||||
Components | EF-P arginine 32 rhamnosyl-transferase | ||||||
Keywords | TRANSFERASE / glycosyltransferase | ||||||
Function / homology | protein-arginine rhamnosyltransferase activity / Protein-arginine rhamnosyltransferase EarP / Elongation-Factor P (EF-P) rhamnosyltransferase EarP / Transferases; Glycosyltransferases; Hexosyltransferases / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE / Protein-arginine rhamnosyltransferase Function and homology information | ||||||
Biological species | Pseudomonas putida KT2440 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.294 Å | ||||||
Authors | Macosek, J. / Krafczyk, R. / Jagtap, P.K.A. / Lassaka, J. / Hennig, J. | ||||||
Citation | Journal: MBio / Year: 2017 Title: Structural Basis for EarP-Mediated Arginine Glycosylation of Translation Elongation Factor EF-P. Authors: Krafczyk, R. / Macosek, J. / Jagtap, P.K.A. / Gast, D. / Wunder, S. / Mitra, P. / Jha, A.K. / Rohr, J. / Hoffmann-Roder, A. / Jung, K. / Hennig, J. / Lassak, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nv8.cif.gz | 139.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nv8.ent.gz | 107.8 KB | Display | PDB format |
PDBx/mmJSON format | 5nv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nv8_validation.pdf.gz | 713.1 KB | Display | wwPDB validaton report |
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Full document | 5nv8_full_validation.pdf.gz | 721.1 KB | Display | |
Data in XML | 5nv8_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 5nv8_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/5nv8 ftp://data.pdbj.org/pub/pdb/validation_reports/nv/5nv8 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43678.191 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria) / Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: earP, PP_1857 / Production host: Escherichia coli (E. coli) / References: UniProt: Q88LS1 |
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#2: Chemical | ChemComp-TRH / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.2M ammonium acetate, 0.1M bis-tris and 27% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8729 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 |
Reflection | Resolution: 2.298→46.542 Å / Num. obs: 17539 / % possible obs: 97.13 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.13 / Rrim(I) all: 0.185 / Χ2: 0.976 / Net I/σ(I): 7.73 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.87 / Num. unique obs: 1760 / CC1/2: 0.68 / Rrim(I) all: 0.929 / % possible all: 98.49 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.294→46.556 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 38.92 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.294→46.556 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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