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- PDB-5a8c: The ultra high resolution structure of a novel alpha-L-arabinofur... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5a8c | ||||||
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Title | The ultra high resolution structure of a novel alpha-L-arabinofuranosidase (CtGH43) from Clostridium thermocellum ATCC 27405 with bound trimethyl N-Oxide (TRS) | ||||||
![]() | CARBOHYDRATE BINDING FAMILY 6 | ||||||
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Function / homology | ![]() polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Goyal, A. / Ahmed, S. / Sharma, K. / Fontes, C.M.G.A. / Najmudin, S. | ||||||
![]() | ![]() Title: Molecular determinants of substrate specificity revealed by the structure of Clostridium thermocellum arabinofuranosidase 43A from glycosyl hydrolase family 43 subfamily 16. Authors: Goyal, A. / Ahmed, S. / Sharma, K. / Gupta, V. / Bule, P. / Alves, V.D. / Fontes, C.M. / Najmudin, S. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2014 Title: Crystallization and Preliminary X-Ray Crystallographic Analysis of a Novel Alpha-L-Arabinofuranosidase (Ctgh43) Fr Clostridium Thermocellum Atcc 27405. Authors: Goyal, A. / Ahmed, S. / Fontes, C.M.G.A. / 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 | ![]() | 156.3 KB | Display | ![]() |
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PDB format | ![]() | 122.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5a8dC ![]() 3c7eS 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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Unit cell |
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Components
#1: Protein | Mass: 36452.402 Da / Num. of mol.: 1 / Fragment: FAMILY 43 GLYCOSIDE HYDROLASE, RESIDUES 30-330 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: A3DEX4, non-reducing end alpha-L-arabinofuranosidase |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-TRS / ![]() |
#4: Water | ChemComp-HOH / ![]() |
Nonpolymer details | CALCIUM ION (CA): FROM THE STORAGE BUFFER 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS): FROM THE ...CALCIUM ION (CA): FROM THE STORAGE BUFFER 2-AMINO-2-HYDROXYMET |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 39 % Description: THE RESOLUTION CUT-OFF TO GET OVER 90 PER CENT COMPLETENESS IS 1.1A BUT ALL THE DATA WAS USED FOR REFINEMENT. |
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Crystal grow![]() | pH: 8.5 Details: 0.1 M TRIS PH 8.5, 20% PEG 2000 MONOMETHYL ETHER, 0.2 M TRIMETHYL N-OXIDE, WITH PARATONE-N USED AS CRYOPROTECTANT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 0.97→67.76 Å / Num. obs: 119795 / % possible obs: 71.5 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 0.97→1 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2 / % possible all: 6.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3C7E Resolution: 0.97→39.95 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.475 / SU ML: 0.011 / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.6 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.11 Å2
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Refinement step | Cycle: LAST / Resolution: 0.97→39.95 Å
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Refine LS restraints |
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