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- PDB-5m2q: Structure of cobinamide-bound BtuF mutant W66F, the periplasmic v... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5m2q | ||||||
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Title | Structure of cobinamide-bound BtuF mutant W66F, the periplasmic vitamin B12 binding protein in E.coli | ||||||
![]() | Outer membrane protein A,Vitamin B12-binding protein | ||||||
![]() | TRANSPORT PROTEIN / BtuF / Cobinamide / periplasmic binding protein / ABC transporter | ||||||
Function / homology | ![]() cobalamin transport complex / outer membrane protein complex / monoatomic ion transmembrane transporter activity / cobalamin transport / detection of virus / outer membrane / cobalamin binding / porin activity / pore complex / monoatomic ion transport ...cobalamin transport complex / outer membrane protein complex / monoatomic ion transmembrane transporter activity / cobalamin transport / detection of virus / outer membrane / cobalamin binding / porin activity / pore complex / monoatomic ion transport / cell outer membrane / outer membrane-bounded periplasmic space / periplasmic space / symbiont entry into host cell / DNA damage response / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mireku, S.A. / Ruetz, M. / Zhou, T. / Korkhov, V.M. / Kraeutler, B. / Locher, K.P. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 206.7 KB | Display | ![]() |
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PDB format | ![]() | 163.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 25.7 KB | Display | |
Data in CIF | ![]() | 36.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5m29SC ![]() 5m34C ![]() 5m3bC 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31472.889 Da / Num. of mol.: 2 / Mutation: W66F Source method: isolated from a genetically manipulated source Details: OmpA-NcoI-BtuF-BamHI-3C-BamHI-His6 / Source: (gene. exp.) ![]() ![]() Gene: ompA, con, tolG, tut, b0957, JW0940, btuF, yadT, b0158, JW0154 Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.32 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: PEG3350 HEPES pH 7 Tryptone |
-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97794 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→19.71 Å / Num. obs: 61170 / % possible obs: 96.27 % / Redundancy: 3.1 % / Net I/σ(I): 11.05 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5M29 Resolution: 1.7→19.71 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.866 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.116 / 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: 33.948 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→19.71 Å
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Refine LS restraints |
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