[English] 日本語
Yorodumi- PDB-2xlc: Acetyl xylan esterase from Bacillus pumilus CECT5072 bound to paraoxon -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xlc | ||||||
---|---|---|---|---|---|---|---|
Title | Acetyl xylan esterase from Bacillus pumilus CECT5072 bound to paraoxon | ||||||
Components | ACETYL XYLAN ESTERASE | ||||||
Keywords | HYDROLASE / CE-7 FAMILY / IRREVERSIBLE INHIBITION | ||||||
Function / homology | Function and homology information acetylesterase / polysaccharide metabolic process / acetylesterase activity Similarity search - Function | ||||||
Biological species | BACILLUS PUMILUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Gil-Ortiz, F. / Montoro-Garcia, S. / Polo, L.M. / Rubio, V. / Sanchez-Ferrer, A. | ||||||
Citation | Journal: Biochem.J. / Year: 2011 Title: The Crystal Structure of the Cephalosporin Deacetylating Enzyme Acetyl Xylan Esterase Bound to Paraoxon Explains the Low Sensitivity of This Serine Hydrolase to Organophosphate Inactivation. Authors: Montoro-Garcia, S. / Gil-Ortiz, F. / Garcia-Carmona, F. / Polo, L.M. / Rubio, V. / Sanchez-Ferrer, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2xlc.cif.gz | 705.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2xlc.ent.gz | 588.5 KB | Display | PDB format |
PDBx/mmJSON format | 2xlc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xlc_validation.pdf.gz | 494.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2xlc_full_validation.pdf.gz | 564 KB | Display | |
Data in XML | 2xlc_validation.xml.gz | 72.1 KB | Display | |
Data in CIF | 2xlc_validation.cif.gz | 95.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/2xlc ftp://data.pdbj.org/pub/pdb/validation_reports/xl/2xlc | HTTPS FTP |
-Related structure data
Related structure data | 2xlbC 1odsS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
|
-Components
#1: Protein | Mass: 36343.340 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS PUMILUS (bacteria) / Strain: CECT5072 / Plasmid: PET28A6HIS-AXE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA (DE3) PLYS / References: UniProt: Q9K5F2, acetylxylan esterase #2: Chemical | ChemComp-DEP / #3: Water | ChemComp-HOH / | Nonpolymer details | DIETHYL PHOSPHATE (DEP): COVALENTLY | Sequence details | SEQUENCE CONFLICTS ARE DUE TO SEQUENCES COMING FROM DIFFERENT BACILLUS PUMILUS STRAINS, PS213 ...SEQUENCE CONFLICTS ARE DUE TO SEQUENCES COMING FROM DIFFERENT BACILLUS PUMILUS STRAINS, PS213 (UNIPROT SEQUENCE) AND CECT 5072 (PDB ENTRY 2XLC) | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45 % / Description: NONE |
---|---|
Crystal grow | pH: 5.5 Details: 0.2 M NH4 ACETATE, 0.1 M BIS-TRIS PH 5.5, 45% 2-METHYL-2,4-PENTANEDIOL (MPD) |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.907 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 10, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.907 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 46958 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 54.137 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.8 / % possible all: 99.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ODS Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.912 / SU B: 30.858 / SU ML: 0.281 / Cross valid method: THROUGHOUT / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.763 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|