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Yorodumi- PDB-1ci8: ESTERASE ESTB FROM BURKHOLDERIA GLADIOLI: AN ESTERASE WITH (BETA)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ci8 | ||||||
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Title | ESTERASE ESTB FROM BURKHOLDERIA GLADIOLI: AN ESTERASE WITH (BETA)-LACTAMASE FOLD. | ||||||
Components | PROTEIN (CARBOXYLESTERASE) | ||||||
Keywords | HYDROLASE / ESTERASE / LACTAMASE FOLD | ||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Burkholderia gladioli (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2 Å | ||||||
Authors | Wagner, U.G. / Petersen, E.I. / Schwab, H. / Kratky, C. | ||||||
Citation | Journal: Protein Sci. / Year: 2002 Title: EstB from Burkholderia gladioli: a novel esterase with a beta-lactamase fold reveals steric factors to discriminate between esterolytic and beta-lactam cleaving activity Authors: Wagner, U.G. / Petersen, E.I. / Schwab, H. / Kratky, C. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1997 Title: Crystallization and preliminary X-ray diffraction studies of the Pseudomonas marginata esterase EstB. Authors: Wagner, U.G. / Solkner, B. / Petersen, E.I. / Schlacher, A. / Schwab, H. / Kratky, C. | ||||||
History |
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Remark 999 | SEQUENCE THE SEQUENCE OF THIS PROTEIN IS NOT AVAILABLE IN SEQUENCE DATABASE |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ci8.cif.gz | 156.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ci8.ent.gz | 124.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ci8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ci8_validation.pdf.gz | 383 KB | Display | wwPDB validaton report |
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Full document | 1ci8_full_validation.pdf.gz | 391.6 KB | Display | |
Data in XML | 1ci8_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 1ci8_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/1ci8 ftp://data.pdbj.org/pub/pdb/validation_reports/ci/1ci8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.992279, -0.005429, 0.12391), Vector: |
-Components
#1: Protein | Mass: 41751.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia gladioli (bacteria) / Cellular location: INTRACELLULAR / Gene: ESTB / Plasmid: PMS470(DELTA)8 / Cellular location (production host): INTRACELLULAR / Production host: Escherichia coli (E. coli) / Strain (production host): E. COLI K12 / References: UniProt: Q9KX40, carboxylesterase #2: Chemical | ChemComp-IPA / #3: Water | ChemComp-HOH / | |
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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: 2.4 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 10% PEG 4000, 10% 2-PROPANOL, 0.05 M NA HEPES BUFFER (PH=7.5), pH 7.50 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 49177 / % possible obs: 68 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.053 |
Reflection shell | Resolution: 1.8→2 Å / Rmerge(I) obs: 0.138 / % possible all: 27 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å / % possible obs: 68 % / Num. measured all: 188976 |
Reflection shell | *PLUS % possible obs: 27 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
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Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Total num. of bins used: 8
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å / Rfactor obs: 0.184 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.293 / Rfactor Rwork: 0.218 |