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Yorodumi- PDB-5m29: Structure of cobinamide-bound BtuF, the periplasmic vitamin B12 b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m29 | ||||||
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Title | Structure of cobinamide-bound BtuF, the periplasmic vitamin B12 binding protein in E.coli | ||||||
Components | Vitamin B12-binding protein | ||||||
Keywords | TRANSPORT PROTEIN / BtuF / Cobinamide / periplasmic binding protein / ABC transporter | ||||||
Function / homology | Function and homology information cobalamin transport complex / cobalamin transport / cobalamin binding / outer membrane-bounded periplasmic space / periplasmic space / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Mireku, S.A. / Ruetz, M. / Zhou, T. / Korkhov, V.M. / Kraeutler, B. / Locher, K.P. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Conformational Change of a Tryptophan Residue in BtuF Facilitates Binding and Transport of Cobinamide by the Vitamin B12 Transporter BtuCD-F. Authors: Mireku, S.A. / Ruetz, M. / Zhou, T. / Korkhov, V.M. / Krautler, B. / Locher, K.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m29.cif.gz | 124.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m29.ent.gz | 93.3 KB | Display | PDB format |
PDBx/mmJSON format | 5m29.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/5m29 ftp://data.pdbj.org/pub/pdb/validation_reports/m2/5m29 | HTTPS FTP |
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-Related structure data
Related structure data | 5m2qC 5m34C 5m3bC 1n2zS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31834.275 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: OmpA-NcoI-BtuF-BamHI-3Csite-BamHI-His6Tag / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: btuF, yadT, b0158, JW0154 / Production host: Escherichia coli (E. coli) / References: UniProt: P37028 #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.61 Å3/Da / Density % sol: 52.81 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: HEPES sodium pH 7.0 PEG3350 Tryptone |
-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 27, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→29.39 Å / Num. obs: 89615 / % possible obs: 96.02 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 10.16 |
Reflection shell | Resolution: 1.5→1.69 Å / Rmerge(I) obs: 0.849 / Num. measured obs: 8600 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1N2Z Resolution: 1.5→29.39 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.661 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.074 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.424 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→29.39 Å
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Refine LS restraints |
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