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Yorodumi- PDB-5luk: Structure of a double variant of cutinase 2 from Thermobifida cel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5luk | |||||||||||||||||||||
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Title | Structure of a double variant of cutinase 2 from Thermobifida cellulosilytica | |||||||||||||||||||||
Components | Cutinase 2 | |||||||||||||||||||||
Keywords | HYDROLASE / cutinase / alpha/beta hydrolase / poly(ethyleneterephthlate) (PET) | |||||||||||||||||||||
Function / homology | Function and homology information poly(ethylene terephthalate) hydrolase / cutinase activity / cutinase / periplasmic space / extracellular region Similarity search - Function | |||||||||||||||||||||
Biological species | Thermobifida cellulosilytica (bacteria) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | |||||||||||||||||||||
Authors | Hromic, A. / Lyskowski, A. / Gruber, K. | |||||||||||||||||||||
Funding support | Austria, 6items
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Citation | Journal: Biotechnol. Bioeng. / Year: 2017 Title: Small cause, large effect: Structural characterization of cutinases from Thermobifida cellulosilytica. Authors: Ribitsch, D. / Hromic, A. / Zitzenbacher, S. / Zartl, B. / Gamerith, C. / Pellis, A. / Jungbauer, A. / yskowski, A. / Steinkellner, G. / Gruber, K. / Tscheliessnig, R. / Herrero Acero, E. / Guebitz, G.M. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5luk.cif.gz | 70.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5luk.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 5luk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/5luk ftp://data.pdbj.org/pub/pdb/validation_reports/lu/5luk | HTTPS FTP |
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-Related structure data
Related structure data | 5luiC 5lujC 5lulC 1jfrS 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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Unit cell |
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-Components
#1: Protein | Mass: 28857.307 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermobifida cellulosilytica (bacteria) Gene: cut2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: E9LVH9 | ||||
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#2: Chemical | #3: Chemical | #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: 1.87 Å3/Da / Density % sol: 34.36 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion Details: 1.1 M Sodium malonate pH 7.0, 0.1 M HEPES pH 7.0, and 0.5% v/v Jeffamine ED-2001 pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9777 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2013 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9777 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→37.9 Å / Num. obs: 38429 / % possible obs: 98 % / Redundancy: 8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.077 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 5 / CC1/2: 0.948 / % possible all: 83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JFR Resolution: 1.45→37.886 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.74
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→37.886 Å
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Refine LS restraints |
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LS refinement shell |
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