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- PDB-4v1l: High resolution structure of a novel carbohydrate binding module ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4v1l | ||||||
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Title | High resolution structure of a novel carbohydrate binding module from glycoside hydrolase family 9 (Cel9A) from Ruminococcus flavefaciens FD-1 | ||||||
![]() | CARBOHYDRATE BINDING MODULE | ||||||
![]() | SUGAR BINDING PROTEIN / CEL9A / CELLULOSOME | ||||||
Function / homology | Domain of unknown function DUF5620 / Domain of unknown function (DUF5620) / TRIETHYLENE GLYCOL / Carbohydrate binding module![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Venditto, I. / Goyal, A. / Thompson, A. / 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.R. / Dourado, C.G. / Ferreira, L.M.A. / 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.R. / Dourado, C.G. / Ferreira, L.M.A. / Coutinho, P.M. / Henrissat, B. / Knox, J.P. / Basle, A. / Najmudin, S. / Gilbert, H.J. / Willats, W.G.T. / Fontes, C.M.G.A. #1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015 Title: Crystallization and preliminary crystallographic studies of a novel noncatalytic carbohydrate-binding module from the Ruminococcus flavefaciens cellulosome. Authors: Venditto, I. / Goyal, A. / Thompson, A. / Ferreira, L.M. / 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 | ![]() | 177.4 KB | Display | ![]() |
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PDB format | ![]() | 142.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 30.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d3lC ![]() 4v17C ![]() 4v18C ![]() 4v1bC ![]() 4v1iC ![]() 4v1kSC ![]() 5aosC ![]() 5aotC ![]() 5fu2C ![]() 5fu3C ![]() 5fu4C ![]() 5fu5C C: citing same article ( 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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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 15329.945 Da / Num. of mol.: 3 / Fragment: CARBOHYDRATE BINDING MODULE, RESIDUES 492-629 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 360 molecules ![](data/chem/img/P6G.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PG4 / | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | TETRAETHYLENE GLYCOL (PG4): JUST BASED ON ELECTRON DENSITY AND IS PROBABLY AN ARTEFACT FROM THE ...TETRAETHYL |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 1 M SODIUM CITRATE, 0.1 M MES PH 6.5, 30% GLYCEROL WAS ADDED IN ABOVE CONDITOIN FOR TEH CRYOPROTECTANT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30.19 Å / Num. obs: 58166 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 11.3 % / Rmerge(I) obs: 1.38 / Mean I/σ(I) obs: 1.8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4V1K Resolution: 1.75→74.83 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.848 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. LIGAND IDENTIFIER FROM PHENIX SUITE AND PDB_REDO WERE USED DURING REFINEMENT. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.966 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→74.83 Å
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Refine LS restraints |
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