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Yorodumi- PDB-4zs9: Raffinose and panose binding protein from Bifidobacterium animali... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zs9 | |||||||||
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Title | Raffinose and panose binding protein from Bifidobacterium animalis subsp. lactis Bl-04, bound with raffinose | |||||||||
Components | Sugar binding protein of ABC transporter system | |||||||||
Keywords | TRANSPORT PROTEIN / Raffinose / ABC transporter / complex | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Bifidobacterium animalis subsp. lactis Bl-04 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å | |||||||||
Authors | Fredslund, F. / Ejby, M. / Andersen, J.M. / Slotboom, D.J. / Abou Hachem, M. | |||||||||
Funding support | Denmark, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2016 Title: An ATP Binding Cassette Transporter Mediates the Uptake of alpha-(1,6)-Linked Dietary Oligosaccharides in Bifidobacterium and Correlates with Competitive Growth on These Substrates. Authors: Ejby, M. / Fredslund, F. / Andersen, J.M. / Vujicic Zagar, A. / Henriksen, J.R. / Andersen, T.L. / Svensson, B. / Slotboom, D.J. / Abou Hachem, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zs9.cif.gz | 469.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zs9.ent.gz | 386.1 KB | Display | PDB format |
PDBx/mmJSON format | 4zs9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/4zs9 ftp://data.pdbj.org/pub/pdb/validation_reports/zs/4zs9 | HTTPS FTP |
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-Related structure data
Related structure data | 4zzaSC 4zzeC 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: 46103.555 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium animalis subsp. lactis Bl-04 (bacteria) Gene: Balac_1599 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): DE3 / References: UniProt: C6A9Y6, UniProt: A0A1A9TA69*PLUS #2: Polysaccharide | #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CL / #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: 2.19 Å3/Da / Density % sol: 43.78 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion / pH: 8.5 Details: 0.1 M Tris pH 8.5, 25% PEG 4000, 0.8 M magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9797 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2012 |
Radiation | Monochromator: Bartels monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→57 Å / Num. obs: 151108 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.37→1.41 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 2.1 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZZA Resolution: 1.37→57 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.12 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.31 Å2 / Biso mean: 19.1672 Å2 / Biso min: 5.61 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.37→57 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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