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Yorodumi- PDB-2xlc: Acetyl xylan esterase from Bacillus pumilus CECT5072 bound to paraoxon -
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Open data
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Basic information
| Entry | Database: PDB / ID: 2xlc | ||||||
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| 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 informationacetylesterase / polysaccharide metabolic process / acetylesterase activity Similarity search - Function | ||||||
| Biological species | ![]() | ||||||
| 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: 2011Title: 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 |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 2xlc.cif.gz | 705 KB | Display | PDBx/mmCIF format |
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| 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 |
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| 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 ( |
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| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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| Unit cell |
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| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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Components
| #1: Protein | Mass: 36343.340 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | ChemComp-DEP / #3: Water | ChemComp-HOH / | Has protein modification | Y | 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) | |
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-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45 % / Description: NONE |
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| 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 |
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| 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 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting 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.
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| 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
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| Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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| Refine LS restraints |
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