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Yorodumi- PDB-4d3l: SeMet structure of a novel carbohydrate binding module from glyco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4d3l | ||||||
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Title | SeMet structure of a novel carbohydrate binding module from glycoside hydrolase family 9 (Cel9A) from Ruminococcus flavefaciens FD-1 in the orthorhombic form | ||||||
Components | CARBOHYDRATE BINDING MODULE | ||||||
Keywords | SUGAR BINDING PROTEIN / CARBOHYDRATE BINDING MODULE / GLYCOSIDE HYDROLASE FAMILY 9 / CEL9A / CELLULOSOME / RUMINOCOCCUS FLAVEFACIENS FD-1 | ||||||
Function / homology | Domain of unknown function DUF5620 / Domain of unknown function (DUF5620) / (3S)-3-HYDROXYHEPTANEDIOIC ACID / DI(HYDROXYETHYL)ETHER / Carbohydrate binding module Function and homology information | ||||||
Biological species | RUMINOCOCCUS FLAVEFACIENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Venditto, I. / Goyal, A. / Thompson, A. / 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: 2015 Title: Crystallization and Preliminary Crystallographic Studies of a Novel, Non-Catalytic Carbohydrate- Binding Module from Ruminococcus Flavefaciens Cellulosome. Authors: Venditto, I. / Goyal, A. / Thompson, A. / 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 | 4d3l.cif.gz | 170.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d3l.ent.gz | 144.2 KB | Display | PDB format |
PDBx/mmJSON format | 4d3l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4d3l_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4d3l_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4d3l_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 4d3l_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/4d3l ftp://data.pdbj.org/pub/pdb/validation_reports/d3/4d3l | HTTPS FTP |
-Related structure data
Related structure data | 4v17C 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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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: 15470.633 Da / Num. of mol.: 3 / Fragment: CARBOHYDRATE BINDING MODULE, RESIDUES 492-629 Source method: isolated from a genetically manipulated source Details: SELENO-METHIONINE DERIVATIVE / Source: (gene. exp.) RUMINOCOCCUS FLAVEFACIENS (bacteria) / Strain: FD-1 / Plasmid: PET-28A / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834(DE3) / References: UniProt: A0A140UH31*PLUS |
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-Non-polymers , 9 types, 244 molecules
#2: Chemical | ChemComp-2PE / | ||||||||
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#3: Chemical | ChemComp-P6G / | ||||||||
#4: Chemical | ChemComp-EDO / | ||||||||
#5: Chemical | ChemComp-GOL / | ||||||||
#6: Chemical | #7: Chemical | ChemComp-CA / | #8: Chemical | ChemComp-PG4 / | #9: Chemical | ChemComp-HHD / ( | #10: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | NONAETHYLENE GLYCOL (2PE): ARTEFACT FROM EXPRESSION, PURIFICATION OR CRYSTALLISATION. BASED PURELY ...NONAETHYLE |
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Sequence details | SELENOMETH |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61 % / Description: PHASER SAD AND PARROT WERE ALSO USED. |
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Crystal grow | pH: 7 Details: 0.2 M SODIUM CITRATE, 2 M AMMONIUM SULPHATE. CRYOPROTECTANT USED PARATONE N, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97895 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97895 Å / Relative weight: 1 |
Reflection | Resolution: 2→43.63 Å / Num. obs: 37050 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 0.9 / % possible all: 69.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2→75.02 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.915 / SU B: 10.187 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED WITH EACH MONOMER DEFINED AS A SINLGE TLS GROUP. PDB_REDO WAS USED IN TH PENULTIMATE REFINEMET ROUND.
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.825 Å2
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Refinement step | Cycle: LAST / Resolution: 2→75.02 Å
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Refine LS restraints |
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