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Yorodumi- PDB-4v1b: Structure of a novel carbohydrate binding module from glycoside h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v1b | ||||||
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Title | Structure of a novel carbohydrate binding module from glycoside hydrolase family 5 glucanase from Ruminococcus flavefaciens FD-1 collected at the Zn edge | ||||||
Components | CARBOHYDRATE BINDING MODULE | ||||||
Keywords | SUGAR BINDING PROTEIN / CELLULOSOME | ||||||
Function / homology | Carbohydrate binding module Function and homology information | ||||||
Biological species | RUMINOCOCCUS FLAVEFACIENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 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 | 4v1b.cif.gz | 126 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4v1b.ent.gz | 101.3 KB | Display | PDB format |
PDBx/mmJSON format | 4v1b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v1b_validation.pdf.gz | 433.7 KB | Display | wwPDB validaton report |
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Full document | 4v1b_full_validation.pdf.gz | 433.8 KB | Display | |
Data in XML | 4v1b_validation.xml.gz | 12 KB | Display | |
Data in CIF | 4v1b_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/4v1b ftp://data.pdbj.org/pub/pdb/validation_reports/v1/4v1b | HTTPS FTP |
-Related structure data
Related structure data | 4d3lC 4v17C 4v18SC 4v1iC 4v1kC 4v1lC 5aosC 5aotC 5fu2C 5fu3C 5fu4C 5fu5C C: citing same article (ref.) S: Starting model for refinement |
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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
#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 / | Sequence details | GB WP009983134 | |
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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 Details: 0.2 M K2SO4, 20% PEG 3350. CRYO 30% GLYCEROL IN THE ABOVE CONDITION, PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.2855 |
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: 1.2855 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→66.13 Å / Num. obs: 9947 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 19.3 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.69→2.76 Å / Redundancy: 19 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 3.2 / % possible all: 99.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4V18 Resolution: 2.69→66.13 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 27.482 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 1.285 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.606 Å2
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Refinement step | Cycle: LAST / Resolution: 2.69→66.13 Å
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Refine LS restraints |
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