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Yorodumi- PDB-5mu5: Structure of MAf glycosyltransferase from Magnetospirillum magnet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mu5 | ||||||
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Title | Structure of MAf glycosyltransferase from Magnetospirillum magneticum AMB-1 | ||||||
Components | Uncharacterized protein | ||||||
Keywords | TRANSFERASE / glycosyltransferase | ||||||
Function / homology | 6-hydroxymethylpterin diphosphokinase MptE-like / 6-hydroxymethylpterin diphosphokinase MptE-like / TRIETHYLENE GLYCOL / Uncharacterized protein Function and homology information | ||||||
Biological species | Magnetospirillum magneticum AMB-1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Sulzenbacher, G. / Roig-Zamboni, V. / Murat, D. / Vincentelli, R. / Wu, L.F. / Guerardel, Y. / Alberto, F. | ||||||
Citation | Journal: Environ. Microbiol. / Year: 2018 Title: Glycosylate and move! The glycosyltransferase Maf is involved in bacterial flagella formation. Authors: Sulzenbacher, G. / Roig-Zamboni, V. / Lebrun, R. / Guerardel, Y. / Murat, D. / Mansuelle, P. / Yamakawa, N. / Qian, X.X. / Vincentelli, R. / Bourne, Y. / Wu, L.F. / Alberto, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mu5.cif.gz | 260.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mu5.ent.gz | 210.5 KB | Display | PDB format |
PDBx/mmJSON format | 5mu5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mu/5mu5 ftp://data.pdbj.org/pub/pdb/validation_reports/mu/5mu5 | HTTPS FTP |
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-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 75168.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Magnetospirillum magneticum AMB-1 (bacteria) Gene: amb0685 / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): Rosetta pLys / References: UniProt: Q2W9I6 |
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-Non-polymers , 6 types, 107 molecules
#2: Chemical | ChemComp-SO4 / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-PGE / | #5: Chemical | ChemComp-PG4 / | #6: Chemical | ChemComp-EDO / #7: 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: 3.21 Å3/Da / Density % sol: 62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 1.5-1.7 M (NH4)2SO4, 5% (v/v) polyethylene glycol 400 and 0.1 M MES buffer, pH 6.5-7.0 PH range: 6.5 - 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 29, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→45.3 Å / Num. obs: 43504 / % possible obs: 99.8 % / Redundancy: 5.1 % / Biso Wilson estimate: 40.9 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.04 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.4 / Num. unique all: 6235 / Num. unique obs: 6235 / Rpim(I) all: 0.369 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→45.3 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 12.053 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.183 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.766 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→45.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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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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