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Yorodumi- PDB-6tpp: Structure of E70A mutant of Rex8A from Paenibacillus barcinonensis. -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tpp | ||||||
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Title | Structure of E70A mutant of Rex8A from Paenibacillus barcinonensis. | ||||||
Components | Reducing-end xylose-releasing exo-oligoxylanase Rex8A | ||||||
Keywords | HYDROLASE / Xylan / Exo-oligoxylanase / Xylanases / Xylooligosaccharides / Xylooligomers / Xylose / Hydrolysis / Polysaccharides / Glycan / Glycan degradation / Xylan degradation / Glycosidase / Carbohydrate metabolism. | ||||||
Function / homology | Function and homology information oligosaccharide reducing-end xylanase / oligosaccharide reducing-end xylanase activity / xylan catabolic process Similarity search - Function | ||||||
Biological species | Paenibacillus barcinonensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å | ||||||
Authors | Jimenez-Ortega, E. / Ramirez-Escudero, M. / Sanz-Aparicio, J. | ||||||
Citation | Journal: Febs J. / Year: 2020 Title: Structural analysis of the reducing-end xylose-releasing exo-oligoxylanase Rex8A from Paenibacillus barcinonensis BP-23 deciphers its molecular specificity. Authors: Jimenez-Ortega, E. / Valenzuela, S. / Ramirez-Escudero, M. / Pastor, F.J. / Sanz-Aparicio, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tpp.cif.gz | 166.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tpp.ent.gz | 131.2 KB | Display | PDB format |
PDBx/mmJSON format | 6tpp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tpp_validation.pdf.gz | 446.9 KB | Display | wwPDB validaton report |
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Full document | 6tpp_full_validation.pdf.gz | 451.1 KB | Display | |
Data in XML | 6tpp_validation.xml.gz | 29.1 KB | Display | |
Data in CIF | 6tpp_validation.cif.gz | 41 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/6tpp ftp://data.pdbj.org/pub/pdb/validation_reports/tp/6tpp | HTTPS FTP |
-Related structure data
Related structure data | 6shyC 6srdSC 6sudC 6to0C 6towC 6trhC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 6 - 382 / Label seq-ID: 6 - 382
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-Components
#1: Protein | Mass: 44465.191 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenibacillus barcinonensis (bacteria) / Gene: rex8A, DFQ00_11062 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0S2UQQ5, oligosaccharide reducing-end xylanase #2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.63 Å3/Da / Density % sol: 53.25 % / Description: Bar |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% PEG 6000, 0.1M HEPES pH 7, 0.2M magnesium chloride, 6% glycerol, 0.01M Hexammine cobalt(III) chloride. Microseeding. Cryoprotectant: ethylene glycol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2016 / Details: KB Mirrors |
Radiation | Monochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→77.63 Å / Num. obs: 24307 / % possible obs: 94.4 % / Redundancy: 3 % / CC1/2: 0.971 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.109 / Rrim(I) all: 0.198 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.64→2.77 Å / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3296 / CC1/2: 0.563 / Rpim(I) all: 0.595 / Rrim(I) all: 0.824 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6SRD Resolution: 2.64→77.63 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.895 / SU B: 14.392 / SU ML: 0.289 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.342 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97 Å2 / Biso mean: 26.787 Å2 / Biso min: 7.74 Å2
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Refinement step | Cycle: final / Resolution: 2.64→77.63 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 13528 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.64→2.709 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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