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- PDB-5lxv: Crystal structure of Ruminococcus flavefaciens scaffoldin C cohes... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5lxv | |||||||||
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Title | Crystal structure of Ruminococcus flavefaciens scaffoldin C cohesin in complex with a dockerin from an uncharacterized CBM-containing protein | |||||||||
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![]() | PROTEIN BINDING / cellulosome / cohesin / dockerin / type I cohesin-dockerin / Coh-Doc / protein-protein interaction | |||||||||
Function / homology | ![]() polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Najmudin, S. / Bule, P. / Fontes, C.M.G.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Single Binding Mode Integration of Hemicellulose-degrading Enzymes via Adaptor Scaffoldins in Ruminococcus flavefaciens Cellulosome. Authors: Bule, P. / Alves, V.D. / Leitao, A. / Ferreira, L.M. / Bayer, E.A. / Smith, S.P. / Gilbert, H.J. / Najmudin, S. / Fontes, C.M. #1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2014 Title: Overexpression, crystallization and preliminary X-ray characterization of Ruminococcus flavefaciens scaffoldin C cohesin in complex with a dockerin from an uncharacterized CBM-containing protein. Authors: Bule, P. / Ruimy-Israeli, V. / Cardoso, V. / Bayer, E.A. / Fontes, C.M. / Najmudin, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 194.3 KB | Display | ![]() |
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PDB format | ![]() | 155.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.9 KB | Display | ![]() |
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Full document | ![]() | 438.9 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 25.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2cclS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 18571.367 Da / Num. of mol.: 2 / Fragment: ScaC Type I cohesin domain, UNP residues 29-204 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: scaC / Production host: ![]() ![]() #2: Protein | Mass: 9791.689 Da / Num. of mol.: 2 / Fragment: Doc3: Type I dockerin domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.1 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.1 M potassium thiocyanate, 30% w/v PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 8, 2014 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.4→59.59 Å / Num. obs: 17195 / % possible obs: 97.6 % / Redundancy: 4 % / CC1/2: 0.985 / Rmerge(I) obs: 0.08 / Net I/σ(I): 51.7 | ||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 2CCL Resolution: 2.4→57 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.903 / SU B: 19.881 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.808 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.22 Å2 / Biso mean: 35.648 Å2 / Biso min: 14.77 Å2
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Refinement step | Cycle: final / Resolution: 2.4→57 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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