[English] 日本語
Yorodumi- PDB-4jj6: Crystal structure of a catalytic mutant of Axe2 (Axe2-H194A), an ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jj6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a catalytic mutant of Axe2 (Axe2-H194A), an acetylxylan esterase from Geobacillus stearothermophilus | ||||||
Components | Acetyl xylan esterase | ||||||
Keywords | HYDROLASE / SGNH hydrolase fold / Acetylxylan Esterase / Catalytic Mutant | ||||||
Function / homology | Function and homology information acetylxylan esterase / acetylxylan esterase activity / xylan catabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Lansky, S. / Alalouf, O. / Solomon, V. / Alhassid, A. / Belrahli, H. / Govada, L. / Chayan, N.E. / Shoham, Y. / Shoham, G. | ||||||
Citation | Journal: To be published Title: To be published Authors: Lansky, S. / Alalouf, O. / Solomon, V. / Alhassid, A. / Belrahli, H. / Govada, L. / Chayan, N.E. / Shoham, Y. / Shoham, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4jj6.cif.gz | 112 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4jj6.ent.gz | 87.6 KB | Display | PDB format |
PDBx/mmJSON format | 4jj6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/4jj6 ftp://data.pdbj.org/pub/pdb/validation_reports/jj/4jj6 | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 24733.459 Da / Num. of mol.: 2 / Mutation: H194A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: axe2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09LX1 #2: Chemical | ChemComp-GOL / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.27 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.0-1.4 M K/Na tartrate, 0.3 M NaCl, 0.1 M imidazole buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.954 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 13, 2012 |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→29.86 Å / Num. all: 60800 / Num. obs: 60764 / % possible obs: 99.92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.8→1.846 Å / % possible all: 99.92 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.86 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.1802 / WRfactor Rwork: 0.1436 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8718 / SU B: 2.301 / SU ML: 0.069 / SU R Cruickshank DPI: 0.0857 / SU Rfree: 0.0905 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 140.6 Å2 / Biso mean: 32.9124 Å2 / Biso min: 17.63 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→29.86 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
|