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Yorodumi- PDB-6hni: The ligand-bound, closed structure of CD0873, a substrate binding... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hni | ||||||
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Title | The ligand-bound, closed structure of CD0873, a substrate binding protein with adhesive properties from Clostridium difficile. | ||||||
Components | ABC-type transport system, sugar-family extracellular solute-binding protein | ||||||
Keywords | TRANSPORT PROTEIN / Substrate binding protein / adhesin / tyrosine binding protein / lipoprotein | ||||||
Function / homology | Function and homology information ABC transporter, substrate-binding protein / ABC transporter substrate binding protein / Response regulator / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Peptoclostridium difficile 630 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Bradshaw, W.J. / Kovacs-Simon, A. / Harmer, N.J. / Michell, S.L. / Acharya, K.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Molecular features of lipoprotein CD0873: A potential vaccine against the human pathogenClostridioides difficile. Authors: Bradshaw, W.J. / Bruxelle, J.F. / Kovacs-Simon, A. / Harmer, N.J. / Janoir, C. / Pechine, S. / Acharya, K.R. / Michell, S.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hni.cif.gz | 143.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hni.ent.gz | 111.5 KB | Display | PDB format |
PDBx/mmJSON format | 6hni.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hn/6hni ftp://data.pdbj.org/pub/pdb/validation_reports/hn/6hni | HTTPS FTP |
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-Related structure data
Related structure data | 6hnjC 6hnkC 3lkvS 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: 33905.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Peptoclostridium difficile 630 (bacteria) Gene: CD630_08730 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q18A65 | ||||
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#2: Chemical | ChemComp-TYR / | ||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PEG / | #5: 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: 2.29 Å3/Da / Density % sol: 46.33 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium HEPES pH 7.5, 20% (w/v) PEG 10,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→55.98 Å / Num. obs: 67816 / % possible obs: 99.9 % / Redundancy: 25 % / CC1/2: 0.997 / Rmerge(I) obs: 0.297 / Rpim(I) all: 0.086 / Rrim(I) all: 0.309 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 17 % / Rmerge(I) obs: 6.455 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3424 / CC1/2: 0.327 / Rpim(I) all: 2.319 / Rrim(I) all: 6.88 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LKV Resolution: 1.35→55.98 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.777 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.05 / 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: 19.074 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→55.98 Å
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Refine LS restraints |
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