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- PDB-2c8n: The Structure of a family 51 arabinofuranosidase, Araf51, from Cl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2c8n | |||||||||
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Title | The Structure of a family 51 arabinofuranosidase, Araf51, from Clostridium thermocellum in complex with 1,3-linked arabinoside of xylobiose. | |||||||||
![]() | ALPHA-L-ARABINOFURANOSIDASE | |||||||||
![]() | HYDROLASE / ARABINOFURANOSIDASE / GLYCOSIDASE / XYLAN / ARABINAN | |||||||||
Function / homology | ![]() arabinan catabolic process / L-arabinose metabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Taylor, E.J. / Smith, N.L. / Turkenburg, J.P. / D'Souza, S. / Gilbert, H.J. / Davies, G.J. | |||||||||
![]() | ![]() Title: Structural Insight Into the Ligand Specificity of a Thermostable Family 51 Arabinofuranosidase, Araf51, from Clostridium Thermocellum. Authors: Taylor, E.J. / Smith, N.L. / Turkenburg, J.P. / D'Souza, S. / Gilbert, H.J. / Davies, G.J. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 578.5 KB | Display | ![]() |
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PDB format | ![]() | 474.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 66.5 KB | Display | |
Data in CIF | ![]() | 99.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2c7fC ![]() 1pz3S 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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4 | ![]()
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5 | ![]()
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6 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 58909.719 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q4CJG5, UniProt: A3DIH0*PLUS, non-reducing end alpha-L-arabinofuranosidase #2: Polysaccharide | alpha-L-arabinofuranose-(1-3)-alpha-D-xylopyranose Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, GLU 173 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 173 TO ALA ...ENGINEERED | Sequence details | THE N-TERMINAL MGSSHHHHHH IS DERIVED FROM THE CLONING VECTOR PET 28A.THE PBD IS NUMBERED AS THE ...THE N-TERMINAL MGSSHHHHHH | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.95 % |
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Crystal grow | Details: 5.0M SODIUM FORMATE,0.1M SODIUM CACODYLATE PH 6.5,5% DIOXANE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 7, 2005 / Details: TORIDAL MIRROR |
Radiation | Monochromator: DIAMOND MOMOCHROMATORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→63.37 Å / Num. obs: 91349 / % possible obs: 99.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.3 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PZ3 Resolution: 2.9→145.86 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.893 / SU B: 36.327 / SU ML: 0.32 / Cross valid method: THROUGHOUT / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.27 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→145.86 Å
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Refine LS restraints |
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