+Open data
-Basic information
Entry | Database: PDB / ID: 5ny0 | ||||||
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Title | L. reuters 100-23 SRRP | ||||||
Components | L. reuteris SRRP binding region | ||||||
Keywords | CELL ADHESION / beta-solenoid / L. reuteri / adhesin | ||||||
Function / homology | L. reuteris SRRP binding region Function and homology information | ||||||
Biological species | Lactobacillus reuteri 100-23 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Sequeira, S. / Dong, C. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Structural basis for the role of serine-rich repeat proteins from Lactobacillus reuteriin gut microbe-host interactions. Authors: Sequeira, S. / Kavanaugh, D. / MacKenzie, D.A. / Suligoj, T. / Walpole, S. / Leclaire, C. / Gunning, A.P. / Latousakis, D. / Willats, W.G.T. / Angulo, J. / Dong, C. / Juge, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ny0.cif.gz | 147.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ny0.ent.gz | 116 KB | Display | PDB format |
PDBx/mmJSON format | 5ny0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/5ny0 ftp://data.pdbj.org/pub/pdb/validation_reports/ny/5ny0 | HTTPS FTP |
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-Related structure data
Related structure data | 5nxkSC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 39439.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus reuteri 100-23 (bacteria) Gene: srrp / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: A0A384E0N5*PLUS |
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#2: 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: 4.74 Å3/Da / Density % sol: 74.02 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 0.2 M sodium tartrate dibasic, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9002 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9002 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→65.06 Å / Num. obs: 37741 / % possible obs: 100 % / Redundancy: 9.2 % / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 5 / Num. unique obs: 5451 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NXK Resolution: 2→49.969 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.19 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→49.969 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -2.4156 Å / Origin y: 27.5352 Å / Origin z: 50.4817 Å
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Refinement TLS group | Selection details: all |