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- PDB-5aos: Structure of a novel carbohydrate binding module from Ruminococcu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5aos | ||||||
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Title | Structure of a novel carbohydrate binding module from Ruminococcus flavefaciens FD-1 endoglucanase Cel5A solved at the As edge | ||||||
![]() | Carbohydrate binding module | ||||||
![]() | SUGAR BINDING PROTEIN / CARBOHYDRATE BINDING MODULE / ENDOGLUCANASE CEL5A / CELLULOSOME / RUMINOCOCCUS FLAVEFACIENS FD-1 / CARBOHYDRATE ACTIVE ENZYME | ||||||
Function / homology | CACODYLATE ION / Carbohydrate binding module![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pires, A.J. / Ribeiro, T. / Thompson, A. / Venditto, I. / Fernandes, V.O. / Bule, P. / Santos, H. / Alves, V.D. / Pires, V. / Ferreira, L.M.A. ...Pires, A.J. / Ribeiro, T. / Thompson, A. / Venditto, I. / Fernandes, V.O. / Bule, P. / Santos, H. / Alves, V.D. / Pires, V. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Najmudin, S. | ||||||
![]() | ![]() Title: Complexity of the Ruminococcus flavefaciens cellulosome reflects an expansion in glycan recognition. Authors: Venditto, I. / Luis, A.S. / Rydahl, M. / Schuckel, J. / Fernandes, V.O. / Vidal-Melgosa, S. / Bule, P. / Goyal, A. / Pires, V.M. / Dourado, C.G. / Ferreira, L.M. / Coutinho, P.M. / ...Authors: Venditto, I. / Luis, A.S. / Rydahl, M. / Schuckel, J. / Fernandes, V.O. / Vidal-Melgosa, S. / Bule, P. / Goyal, A. / Pires, V.M. / Dourado, C.G. / Ferreira, L.M. / Coutinho, P.M. / Henrissat, B. / Knox, J.P. / Basle, A. / Najmudin, S. / Gilbert, H.J. / Willats, W.G. / Fontes, C.M. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2015 Title: Purification and Crystallographic Studies of a Putative Carbohydrate-Binding Module from the Ruminococcus Flavefaciens Fd-1 Endoglucanase Cel5A. Authors: Pires, A.J. / Ribeiro, T. / Thompson, A. / Venditto, I. / Fernandes, V.O. / Bule, P. / Santos, H. / Alves, V.D. / Pires, V. / Ferreira, L.M.A. / Fontes, C.M.G.A. / 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 | ![]() | 59.2 KB | Display | ![]() |
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PDB format | ![]() | 43.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.4 KB | Display | ![]() |
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Full document | ![]() | 446.8 KB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 10.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d3lC ![]() 4v17C ![]() 4v18C ![]() 4v1bC ![]() 4v1iC ![]() 4v1kC ![]() 4v1lC ![]() 5aotC ![]() 5fu2C ![]() 5fu3C ![]() 5fu4C ![]() 5fu5C 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: 11806.894 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE BINDING MODULE, UNP RESIDUES 28-127 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-CAC / | ||||||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Nonpolymer details | CACODYLATE | Sequence details | TRUNCATED AT C-TERMINAL | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 34 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 20 MG/ML PROTEIN IN.2 M SODIUM ACETATE, 0.1 M CACODYLIC ACID PH 6.5, 30%(W/V) POLYETHYLENE GLYCOL 8000. 30%(V/V) GLYCEROL ADDED TO THE CRYSTALLIZATION BUFFER AS CRYOPROTECTANT |
-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: 1.04408 Å / Relative weight: 1 |
Reflection | Resolution: 1.29→33.4 Å / Num. obs: 25196 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 1.29→1.34 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 8.4 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 1.29→33.4 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.998 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. PDB_REDO WAS USED FOR VALIDATING IN THE FINAL ROUND OF REFINEMENT. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.248 Å2
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Refinement step | Cycle: LAST / Resolution: 1.29→33.4 Å
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Refine LS restraints |
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