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Yorodumi- PDB-4ccy: Crystal structure of carboxylesterase CesB (YbfK) from Bacillus s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ccy | ||||||
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Title | Crystal structure of carboxylesterase CesB (YbfK) from Bacillus subtilis | ||||||
Components | (CARBOXYLESTERASE YBFK) x 2 | ||||||
Keywords | HYDROLASE / ALPHA/BETA HYDROLASE | ||||||
Function / homology | Function and homology information methyl indole-3-acetate esterase activity / carboxylesterase / cytoplasm Similarity search - Function | ||||||
Biological species | BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | ||||||
Authors | Rozeboom, H.J. / Godinho, L.F. / Nardini, M. / Quax, W.J. / Dijkstra, B.W. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2014 Title: Crystal Structures of Two Bacillus Carboxylesterases with Different Enantioselectivities. Authors: Rozeboom, H.J. / Godinho, L.F. / Nardini, M. / Quax, W.J. / Dijkstra, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ccy.cif.gz | 240.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ccy.ent.gz | 193.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ccy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ccy_validation.pdf.gz | 432 KB | Display | wwPDB validaton report |
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Full document | 4ccy_full_validation.pdf.gz | 433.6 KB | Display | |
Data in XML | 4ccy_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 4ccy_validation.cif.gz | 38.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/4ccy ftp://data.pdbj.org/pub/pdb/validation_reports/cc/4ccy | HTTPS FTP |
-Related structure data
Related structure data | 4ccwSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 5 / Auth seq-ID: 12 - 294 / Label seq-ID: 11 - 293
NCS oper: (Code: given Matrix: (0.3145, 0.001922, -0.9493), Vector: |
-Components
#1: Protein | Mass: 33118.539 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-296 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria) Plasmid: PBAD/MYC-HISA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10 / References: UniProt: O31452, carboxylesterase | ||
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#2: Protein | Mass: 33102.539 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-296 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria) Plasmid: PBAD/MYC-HISA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10 / References: UniProt: O31452, carboxylesterase | ||
#3: Chemical | ChemComp-NA / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6.5 Details: SITTING DROPS WITH 20% PEG3350, 0.2M SODIUM FLUORIDE, 100 MM BIS-TRIS PROPANE BUFFER, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 5, 2011 / Details: HELIOSMX |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→46 Å / Num. obs: 47148 / % possible obs: 92.8 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.04→2.14 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.9 / % possible all: 76.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CCW Resolution: 2.04→108.6 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.889 / SU B: 8.309 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.127 Å2
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Refinement step | Cycle: LAST / Resolution: 2.04→108.6 Å
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Refine LS restraints |
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