[English] 日本語
Yorodumi- PDB-3mua: Enzyme-Substrate interactions of IXT6, the intracellular xylanase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mua | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Enzyme-Substrate interactions of IXT6, the intracellular xylanase of G. stearothermophilus. | |||||||||
Components | Xylanase | |||||||||
Keywords | HYDROLASE / Intracellular xylanase / xylotriose | |||||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process Similarity search - Function | |||||||||
Biological species | Geobacillus stearothermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å | |||||||||
Authors | Solomon, V. / Zolotnitsky, G. / Alhadeff, R. / Shoham, Y. / Shoham, G. | |||||||||
Citation | Journal: TO BE PUBLISHED Title: Enzyme-Substrate interactions of IXT6, the intracellular xylanase of G. stearothermophilus. Authors: Solomon, V. / Zolotnitsky, G. / Alhadeff, R. / Shoham, Y. / Shoham, G. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3mua.cif.gz | 166.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3mua.ent.gz | 129.2 KB | Display | PDB format |
PDBx/mmJSON format | 3mua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mu/3mua ftp://data.pdbj.org/pub/pdb/validation_reports/mu/3mua | HTTPS FTP |
---|
-Related structure data
Related structure data | 3ms8C 3msdC 3msgC 3muiC 2q8xS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 38695.852 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Strain: T-6 / Gene: xynA2 / Plasmid: pET9d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: Q3YBZ9, UniProt: Q09LY9*PLUS, endo-1,4-beta-xylanase |
---|
-Sugars , 2 types, 3 molecules
#2: Polysaccharide | #3: Sugar | ChemComp-XYP / | |
---|
-Non-polymers , 4 types, 626 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.75 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M sodium cacodylate pH 6.5, 1.9M sodium acetate, 40mM xylotriose., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 14, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→39.56 Å / Num. obs: 169396 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 20.9 Å2 / Rsym value: 0.075 / Net I/σ(I): 22.38 |
Reflection shell | Resolution: 1.5→1.53 Å / Mean I/σ(I) obs: 2.98 / Num. unique all: 8457 / Rsym value: 0.453 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: 2Q8X Resolution: 1.5→39.56 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.4 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→39.56 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.008
|