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Yorodumi- PDB-4v17: Structure of a novel carbohydrate binding module from glycoside h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v17 | ||||||
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Title | Structure of a novel carbohydrate binding module from glycoside hydrolase family 5 glucanase from Ruminococcus flavefaciens FD-1 | ||||||
Components | CARBOHYDRATE BINDING MODULE | ||||||
Keywords | SUGAR BINDING PROTEIN | ||||||
Function / homology | Carbohydrate binding module Function and homology information | ||||||
Biological species | RUMINOCOCCUS FLAVEFACIENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Venditto, I. / Centeno, M.S.J. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Najmudin, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 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.,Sect.F / Year: 2014 Title: Expression, Purification and Crystallization of a Novel Carbohydrate-Binding Module from the Ruminococcus Flavefaciens Cellulosome. Authors: Venditto, I. / Centeno, M.S.J. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Najmudin, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v17.cif.gz | 128.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4v17.ent.gz | 102.6 KB | Display | PDB format |
PDBx/mmJSON format | 4v17.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v17_validation.pdf.gz | 442.3 KB | Display | wwPDB validaton report |
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Full document | 4v17_full_validation.pdf.gz | 447.4 KB | Display | |
Data in XML | 4v17_validation.xml.gz | 14 KB | Display | |
Data in CIF | 4v17_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/4v17 ftp://data.pdbj.org/pub/pdb/validation_reports/v1/4v17 | HTTPS FTP |
-Related structure data
Related structure data | 4d3lC 4v18C 4v1bC 4v1iC 4v1kC 4v1lC 5aosC 5aotC 5fu2C 5fu3C 5fu4C 5fu5C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17273.186 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RUMINOCOCCUS FLAVEFACIENS (bacteria) / Strain: FD-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: A0A140UH28*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 1.2 M NA2 CITRATE, 0.1 M HEPES PH 7.5 CRYO 30% GLYCEROL IN ABOVE CONDITION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2→30.17 Å / Num. obs: 26385 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 16.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 15.2 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.7 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SEMET DERIVATIVE FROM 2.28 A Resolution: 2→77.16 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 11.653 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.336 Å2
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Refinement step | Cycle: LAST / Resolution: 2→77.16 Å
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Refine LS restraints |
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