+Open data
-Basic information
Entry | Database: PDB / ID: 6zt6 | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure of mutated arabinofuranosidase | ||||||
Components | Alpha-L-arabinofuranosidase | ||||||
Keywords | HYDROLASE / Transferase | ||||||
Function / homology | Alpha-L-arabinofuranosidase, C-terminal / Alpha-L-arabinofuranosidase C-terminal domain / Alpha-L-arabinofuranosidase C-terminus / L-arabinose metabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / Alpha-L-arabinofuranosidase Function and homology information | ||||||
Biological species | Thermobacillus xylanilyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Tandrup, T. / Lo Leggio, L. / Zhao, J. / Bissaro, B. / Barbe, S. / Andre, I. / Dumon, C. / O'Donohue, M.J. / Faure, R. | ||||||
Citation | Journal: N Biotechnol / Year: 2021 Title: Probing the determinants of the transglycosylation/hydrolysis partition in a retaining alpha-l-arabinofuranosidase. Authors: Zhao, J. / Tandrup, T. / Bissaro, B. / Barbe, S. / Poulsen, J.N. / Andre, I. / Dumon, C. / Lo Leggio, L. / O'Donohue, M.J. / Faure, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6zt6.cif.gz | 339.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6zt6.ent.gz | 275.2 KB | Display | PDB format |
PDBx/mmJSON format | 6zt6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/6zt6 ftp://data.pdbj.org/pub/pdb/validation_reports/zt/6zt6 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6zt7C 6zt8C 6zt9C 6ztaC 2vrqS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0 / Auth seq-ID: 4 - 496 / Label seq-ID: 4 - 496
NCS ensembles :
|
-Components
#1: Protein | Mass: 56155.215 Da / Num. of mol.: 3 / Mutation: R69H, L352M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermobacillus xylanilyticus (bacteria) Gene: AbjA / Production host: Escherichia coli (E. coli) References: UniProt: O69262, non-reducing end alpha-L-arabinofuranosidase #2: Chemical | ChemComp-MPD / ( #3: Chemical | ChemComp-BTB / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.94 Å3/Da / Density % sol: 68.76 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M ammonium acetate, 0.1 M Bis-tris pH 5.5, 45% (v/v) MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.99 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 120575 / % possible obs: 100 % / Redundancy: 16.9 % / CC1/2: 0.99 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.3→2.36 Å / Num. unique obs: 8781 / CC1/2: 0.797 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VRQ Resolution: 2.3→49 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.741 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 307.83 Å2 / Biso mean: 35.93 Å2 / Biso min: 11.08 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→49 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|