[English] 日本語
![](img/lk-miru.gif)
- PDB-3fvt: Crystal Structure of Acetyl Xylan Esterase from Bacillus pumilus,... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3fvt | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Acetyl Xylan Esterase from Bacillus pumilus, monoclinic crystal form II | ||||||
![]() | Acetyl xylan esterase | ||||||
![]() | HYDROLASE / alpha/beta hydrolase / carbohydrate esterase / CE7 / Bacillus pumilus | ||||||
Function / homology | ![]() acetylesterase / polysaccharide metabolic process / acetylesterase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Krastanova, I. / Cassetta, A. / Lamba, D. | ||||||
![]() | ![]() Title: Structural and functional studies of Bacillus pumilus acetyl xylan esterase Authors: Krastanova, I. / Cassetta, A. / Mastihubova, M. / Biely, P. / Lamba, D. #1: ![]() Title: Heterologous expression, purification, crystallization, X-ray analysis and phasing of the acetyl xylan esterase from Bacillus pumilus Authors: Krastanova, I. / Guarnaccia, C. / Zahariev, S. / Degrassi, G. / Lamba, D. #2: ![]() Title: The acetyl xylan esterase of Bacillus pumilus belongs to a family of esterases with broad substrate specificity Authors: Degrassi, G. / Kojic, M. / Ljubijankic, G. / Venturi, V. #3: ![]() Title: Purification and characterization of an acetyl xylan esterase from Bacillus pumilus Authors: Degrassi, G. / Okeke, B.C. / Bruschi, C.V. / Venturi, V. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 804.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 662.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 485.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 541.6 KB | Display | |
Data in XML | ![]() | 77.7 KB | Display | |
Data in CIF | ![]() | 132.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3fvrC ![]() 3fytC ![]() 3fyuC ![]() 1odsS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 36114.844 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CL / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.16 % |
---|---|
Crystal grow | Temperature: 293 K / Method: microbatch / pH: 6 Details: 0.5M lithium chloride, 5% PEG 6000, 0.1M MES, pH 6.0, microbatch, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 31, 2002 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.278 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→29.75 Å / Num. all: 298796 / Num. obs: 298796 / % possible obs: 89.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 22.73 Å2 / Rmerge(I) obs: 0.085 / Χ2: 1.116 |
Reflection shell | Resolution: 1.9→1.91 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 2 / Num. unique all: 9621 / Χ2: 1 / % possible all: 80.7 |
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1ODS Resolution: 1.9→29.74 Å / Rfactor Rfree error: 0.002 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 960989 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.807 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.62 Å2 / Biso mean: 22.086 Å2 / Biso min: 2.22 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→29.74 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|