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- PDB-5n5p: Crystal structure of Ruminococcus flavefaciens' type III complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5n5p | |||||||||
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Title | Crystal structure of Ruminococcus flavefaciens' type III complex containing the fifth cohesin from scaffoldin B and the dockerin from scaffoldin A | |||||||||
![]() | (Putative cellulosomal scaffoldin protein) x 2 | |||||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() polysaccharide catabolic process / ![]() Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Bule, P. / Carvalho, A.L. / Najmudin, S. / Fontes, C.M.G.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Higher order scaffoldin assembly in Ruminococcus flavefaciens cellulosome is coordinated by a discrete cohesin-dockerin interaction. Authors: Bule, P. / Pires, V.M.R. / Alves, V.D. / Carvalho, A.L. / Prates, J.A.M. / Ferreira, L.M.A. / Smith, S.P. / Gilbert, H.J. / Noach, I. / Bayer, E.A. / Najmudin, S. / Fontes, C.M.G.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 181.8 KB | Display | ![]() |
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PDB format | ![]() | 145.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5lxvS 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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1 | ![]()
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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: 0 / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0
NCS ensembles :
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Components
#1: Protein | Mass: 14252.957 Da / Num. of mol.: 2 Fragment: ScaB Type III cohesin domain, UNP residues 739-876 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: scaB / Plasmid: pET28a / Production host: ![]() ![]() ![]() #2: Protein | Mass: 9220.265 Da / Num. of mol.: 2 Fragment: ScaA Type III dockerin domain, UNP residues 648-730 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: scaA / Plasmid: pET28a / Production host: ![]() ![]() ![]() #3: Chemical | ChemComp-CCN / | ![]() #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.35 % / Mosaicity: 0.31 ° |
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Crystal grow![]() | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 0.1M HEPES 7.5, 1.2M Sodium Citrate, 4% v/v Acetonitrile |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2014 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.4→47.63 Å / Num. obs: 26512 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.04 / Rrim(I) all: 0.106 / Net I/σ(I): 8.8 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5lxv Resolution: 1.98→46.58 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.114 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.035 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.41 Å2 / Biso mean: 33.69 Å2 / Biso min: 17.41 Å2
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Refinement step | Cycle: final / Resolution: 1.98→46.58 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: 1.976→2.027 Å / Rfactor Rfree error: 0 / 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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