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Yorodumi- PDB-8puj: The surface-exposed lipo-protein of BtuG2 in complex with cyanoco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8puj | ||||||
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Title | The surface-exposed lipo-protein of BtuG2 in complex with cyanocobalamin. | ||||||
Components | YncE family protein | ||||||
Keywords | TRANSPORT PROTEIN / B12 / transport / soluble protein | ||||||
Function / homology | Protein of unknown function DUF5074 / Domain of unknown function (DUF5074) / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / WD40/YVTN repeat-like-containing domain superfamily / COB(II)INAMIDE / HYDROXIDE ION / YncE family protein Function and homology information | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Whittaker, J. / Martinez-Felices, J.M. / Guskov, A. / Slotboom, D.J. | ||||||
Funding support | Netherlands, 1items
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Citation | Journal: To Be Published Title: The surface-exposed lipo-protein of BtuG3 in complex with cyanocobinamide. Authors: Whittaker, J. / Guskov, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8puj.cif.gz | 158.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8puj.ent.gz | 120.6 KB | Display | PDB format |
PDBx/mmJSON format | 8puj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/8puj ftp://data.pdbj.org/pub/pdb/validation_reports/pu/8puj | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37234.906 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: BSIG_3269 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0F756 #2: Chemical | ChemComp-OH / | #3: Chemical | ChemComp-CBY / | #4: Chemical | ChemComp-NA / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.51 Å3/Da / Density % sol: 51.07 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: 0.2 M potassium nitrate, pH 6.9 20 % (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8731 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→44.02 Å / Num. obs: 83219 / % possible obs: 99.54 % / Redundancy: 9.5 % / CC1/2: 0.95 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.7→1.76 Å / Num. unique obs: 8063 / CC1/2: 0.85 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→44.02 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.77 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→44.02 Å
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Refine LS restraints |
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LS refinement shell |
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