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Yorodumi- PDB-5lul: Structure of a triple variant of cutinase 2 from Thermobifida cel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lul | |||||||||||||||||||||
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Title | Structure of a triple 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: 1.9 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 | 5lul.cif.gz | 120.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lul.ent.gz | 93 KB | Display | PDB format |
PDBx/mmJSON format | 5lul.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/5lul ftp://data.pdbj.org/pub/pdb/validation_reports/lu/5lul | HTTPS FTP |
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-Related structure data
Related structure data | 5luiC 5lujC 5lukC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28787.189 Da / Num. of mol.: 2 / Mutation: R19S, R29N, A30V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermobifida cellulosilytica (bacteria) Gene: cut2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3) / Variant (production host): gold / References: UniProt: E9LVH9 #2: Chemical | ChemComp-CA / | #3: Chemical | ChemComp-CL / | #4: 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: 2.3 Å3/Da / Density % sol: 46.58 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M of each carboxylic acid (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M trisodium citrate, 0.2 M sodium potassium L- ...Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M of each carboxylic acid (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M trisodium citrate, 0.2 M sodium potassium L-tartrate, 0.2 M sodium oxamate) and 0.1 M MOPS/HEPES-Na pH 7.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.8726 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: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→44.53 Å / Num. obs: 41912 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 14 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 11.1 / CC1/2: 0.978 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JFR Resolution: 1.9→44.53 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→44.53 Å
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Refine LS restraints |
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LS refinement shell |
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