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Yorodumi- PDB-3vis: Crystal structure of cutinase Est119 from Thermobifida alba AHK119 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vis | ||||||
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Title | Crystal structure of cutinase Est119 from Thermobifida alba AHK119 | ||||||
Components | Esterase | ||||||
Keywords | HYDROLASE / alpha/beta-hydrolase fold / esterase / polyethylene terephthalate | ||||||
Function / homology | Function and homology information poly(ethylene terephthalate) hydrolase / cutinase activity / cutinase / periplasmic space / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Thermobifida alba (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD, molecular replacement / Resolution: 1.76 Å | ||||||
Authors | Kitadokoro, K. / Thumarat, U. / Nakamura, R. / Nishimura, K. / Karatani, H. / Suzuki, H. / Kawai, F. | ||||||
Citation | Journal: POLYM.DEGRAD.STAB. / Year: 2012 Title: Crystal structure of cutinase Est119 from Thermobida alba AHK119 that can degrade modpolyethylene terephthalate at 1.76 A resolution. Authors: Kitadokoro, K. / Thumarat, U. / Nakamura, R. / Nishimura, K. / Karatani, H. / Suzuki, H. / Kawai, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vis.cif.gz | 211.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vis.ent.gz | 177.3 KB | Display | PDB format |
PDBx/mmJSON format | 3vis.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/3vis ftp://data.pdbj.org/pub/pdb/validation_reports/vi/3vis | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33215.188 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermobifida alba (bacteria) / Strain: AHK119 / Gene: est2 / Plasmid: pQE80L-est119 / Production host: Escherichia coli (E. coli) / References: UniProt: F7IX06 #2: Chemical | ChemComp-PE4 / | #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 grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 25% (w/v) PEG 1000, 0.2M sodium chloride, 0.1M sodium potassium phosphate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jun 24, 2011 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→56.8 Å / Num. all: 44072 / Num. obs: 41770 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.099 |
Reflection shell | Resolution: 1.76→1.82 Å / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: SAD, molecular replacement / Resolution: 1.76→56.75 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.559 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.825 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→56.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.762→1.808 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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