[English] 日本語
Yorodumi- PDB-5gqe: Crystal structure of michaelis complex of xylanase mutant (T82A, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gqe | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of michaelis complex of xylanase mutant (T82A, N127S, and E128H) from Streptomyces olivaceoviridis E-86 | |||||||||
Components | Beta-xylanase | |||||||||
Keywords | HYDROLASE / XYLOPENTAOSE / ES COMPLEX | |||||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / polysaccharide catabolic process Similarity search - Function | |||||||||
Biological species | Streptomyces olivaceoviridis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Suzuki, R. / Fujimoto, Z. / Kaneko, S. / Kuno, A. | |||||||||
Citation | Journal: J.Appl.Glyosci. / Year: 2019 Title: Azidolysis by the Formation of Stable Ser-His Catalytic Dyad in a Glycoside Hydrolase Family 10 Xylanase Mutant Authors: Suzuki, R. / Fujimoto, Z. / Kaneko, S. / Hasegawa, T. / Kuno, A. #1: Journal: J. Biochem. / Year: 2009 Title: Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86. Authors: Suzuki, R. / Fujimoto, Z. / Ito, S. / Kawahara, S. / Kaneko, S. / Taira, K. / Hasegawa, T. / Kuno, A. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5gqe.cif.gz | 196.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5gqe.ent.gz | 153.2 KB | Display | PDB format |
PDBx/mmJSON format | 5gqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gqe_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5gqe_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5gqe_validation.xml.gz | 40.3 KB | Display | |
Data in CIF | 5gqe_validation.cif.gz | 60.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/5gqe ftp://data.pdbj.org/pub/pdb/validation_reports/gq/5gqe | HTTPS FTP |
-Related structure data
Related structure data | 5gqdC 2d1zS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
-Protein / Non-polymers , 2 types, 729 molecules AB
#1: Protein | Mass: 46743.207 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces olivaceoviridis (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7SI98, endo-1,4-beta-xylanase #6: Water | ChemComp-HOH / | |
---|
-Sugars , 4 types, 6 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose | Source method: isolated from a genetically manipulated source #4: Polysaccharide | #5: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylotriose | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.44 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 / Details: 2% McIlvaine buffer 25% Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 173 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Feb 18, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 33186 / % possible obs: 96.3 % / Redundancy: 4.1 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 5.82 / % possible all: 97.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2D1Z Resolution: 2.5→39.16 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3308859.82 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Bsol: 63.9476 Å2 / ksol: 0.40985 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→39.16 Å /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|