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- PDB-6srd: Structure of Rex8A from Paenibacillus barcinonensis complexed wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6srd | |||||||||
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Title | Structure of Rex8A from Paenibacillus barcinonensis complexed with xylose. | |||||||||
![]() | Reducing-end xylose-releasing exo-oligoxylanase Rex8A | |||||||||
![]() | HYDROLASE / Xylan / Exo-oligoxylanase / Xylanases / Xylooligosaccharides / Xylooligomers / Xylose / Hydrolysis / Polysaccharides / Glycan / Glycan degradation / Xylan degradation / Glycosidase / Carbohydrate metabolism. | |||||||||
Function / homology | ![]() oligosaccharide reducing-end xylanase / oligosaccharide reducing-end xylanase activity / xylan catabolic process Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Jimenez-Ortega, E. / Ramirez-Escudero, M. / Sanz-Aparicio, J. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 177.3 KB | Display | ![]() |
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PDB format | ![]() | 138.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 33.6 KB | Display | |
Data in CIF | ![]() | 50.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6shyC ![]() 6sudC ![]() 6to0C ![]() 6towC ![]() 6tppC ![]() 6trhC ![]() 1wu4S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 44523.223 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A0S2UQQ5, oligosaccharide reducing-end xylanase #2: Sugar | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.61 % / Description: Bar |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 23% PEG 6K, 0.1 M Tris pH 8.0, 0.2 M NaCl, 0.01 M Hexammine cobalt (III) chrloride. Soaking experiment in the precipitant solution supplemented with 50 mM xylose. Cryoprotectan solution ...Details: 23% PEG 6K, 0.1 M Tris pH 8.0, 0.2 M NaCl, 0.01 M Hexammine cobalt (III) chrloride. Soaking experiment in the precipitant solution supplemented with 50 mM xylose. Cryoprotectan solution consisting of mother liquor plus 25% (v/v) glycerol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2015 / 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: 1.04191 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→48.63 Å / Num. obs: 64154 / % possible obs: 96.4 % / Redundancy: 3.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.078 / Rrim(I) all: 0.148 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.93→1.98 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 2 / Num. unique obs: 4213 / CC1/2: 0.663 / Rpim(I) all: 0.489 / Rrim(I) all: 0.879 / % possible all: 93.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1WU4 Resolution: 1.93→48.63 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.819 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.153 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: 55.4 Å2 / Biso mean: 16.208 Å2 / Biso min: 5.37 Å2
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Refinement step | Cycle: final / Resolution: 1.93→48.63 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 13932 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.93→1.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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