+Open data
-Basic information
Entry | Database: PDB / ID: 5.0E+75 | ||||||
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Title | Crystal structure of Bacova_02651 | ||||||
Components | SusD-like protein BACOVA_02651 | ||||||
Keywords | SUGAR BINDING PROTEIN / SusD homolog | ||||||
Function / homology | Function and homology information symbiotic process benefiting host / xyloglucan catabolic process / polysaccharide binding / cell outer membrane Similarity search - Function | ||||||
Biological species | Bacteroides ovatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å | ||||||
Model details | SusD homolog | ||||||
Authors | Koropatkin, N.M. | ||||||
Citation | Journal: Mbio / Year: 2016 Title: Molecular Dissection of Xyloglucan Recognition in a Prominent Human Gut Symbiont. Authors: Tauzin, A.S. / Kwiatkowski, K.J. / Orlovsky, N.I. / Smith, C.J. / Creagh, A.L. / Haynes, C.A. / Wawrzak, Z. / Brumer, H. / Koropatkin, N.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e75.cif.gz | 208.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e75.ent.gz | 166.1 KB | Display | PDB format |
PDBx/mmJSON format | 5e75.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/5e75 ftp://data.pdbj.org/pub/pdb/validation_reports/e7/5e75 | HTTPS FTP |
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-Related structure data
Related structure data | 5e76C 5e7gC 5e7hC 3jysS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-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: 59170.430 Da / Num. of mol.: 1 / Fragment: UNP residues 28-546 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153) (bacteria) Strain: ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153 / Gene: BACOVA_02651 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) pLysS / References: UniProt: A7LXT5 |
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-Non-polymers , 6 types, 454 molecules
#2: Chemical | ChemComp-PEG / | ||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #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: 2.04 Å3/Da / Density % sol: 39.75 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Molecular Dimensions Morpheus screen well A1 / Temp details: cold room |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 10, 2014 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→21.48 Å / Num. obs: 99136 / % possible obs: 99.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.04759 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.36→1.409 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.4513 / Mean I/σ(I) obs: 2.29 / % possible all: 98.82 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3JYS Resolution: 1.36→21.48 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.53 / 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: 68.56 Å2 / Biso mean: 17.099 Å2 / Biso min: 7.16 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.36→21.48 Å
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Refine LS restraints |
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LS refinement shell |
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