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- PDB-5m2o: R. flavefaciens' third ScaB cohesin in complex with a group 1 dockerin -
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Open data
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Basic information
Entry | Database: PDB / ID: 5m2o | |||||||||
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Title | R. flavefaciens' third ScaB cohesin in complex with a group 1 dockerin | |||||||||
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![]() | PROTEIN BINDING / Cohesin / Dockerin / Complex / Cellulosome / R. flavefaciens / Structural protein | |||||||||
Function / homology | ![]() polysaccharide catabolic process / carbohydrate binding / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bule, P. / Najmudin, S. / Carvalho, A.L. / Fontes, C.M.G.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Assembly of Ruminococcus flavefaciens cellulosome revealed by structures of two cohesin-dockerin complexes. Authors: Bule, P. / Alves, V.D. / Israeli-Ruimy, V. / Carvalho, A.L. / Ferreira, L.M. / Smith, S.P. / Gilbert, H.J. / Najmudin, S. / Bayer, E.A. / Fontes, C.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.8 KB | Display | ![]() |
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PDB format | ![]() | 82.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 416.8 KB | Display | ![]() |
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Full document | ![]() | 416.8 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 19.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5m2sC ![]() 5aozS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15952.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: scaB / Production host: ![]() ![]() | ||
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#2: Protein | Mass: 10283.526 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.75 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M ammonium nitrate, 20% w/v PEG 3550 |
-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: 1.26→20.27 Å / Num. obs: 62659 / % possible obs: 99.6 % / Redundancy: 7.4 % / CC1/2: 0.976 / Rmerge(I) obs: 0.243 / Rpim(I) all: 0.094 / Rrim(I) all: 0.261 / Net I/σ(I): 5.7 / Num. measured all: 461036 / Scaling rejects: 434 | ||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5aoz Resolution: 1.26→20.27 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.221 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.036 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.21 Å2 / Biso mean: 8.919 Å2 / Biso min: 2.99 Å2
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Refinement step | Cycle: final / Resolution: 1.26→20.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.26→1.293 Å / Total num. of bins used: 20
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Refinement TLS params. | T13: -0.0001 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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