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Yorodumi- PDB-6wpy: Crystal structure of Bacillus licheniformis lipase BlEst2 in matu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wpy | |||||||||
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Title | Crystal structure of Bacillus licheniformis lipase BlEst2 in mature form | |||||||||
Components | BlEst2 | |||||||||
Keywords | HYDROLASE / esterase / lipase / propetide | |||||||||
Function / homology | Alpha/Beta hydrolase fold / Lipase Function and homology information | |||||||||
Biological species | Bacillus licheniformis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å | |||||||||
Authors | Nakamura, A.M. / Godoy, A.S. / Kadowaki, M.A.S. / Polikarpov, I. | |||||||||
Funding support | Brazil, 2items
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Citation | Journal: Febs J. / Year: 2024 Title: Structures of BlEst2 from Bacillus licheniformis in its propeptide and mature forms reveal autoinhibitory effects of the C-terminal domain Authors: Nakamura, A.M. / Godoy, A.S. / Kadowaki, M.A.S. / Trentin, L.N. / Gonzalez, S.E.T. / Skaf, M.S. / Polikarpov, I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wpy.cif.gz | 311.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wpy.ent.gz | 244.8 KB | Display | PDB format |
PDBx/mmJSON format | 6wpy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wpy_validation.pdf.gz | 469.2 KB | Display | wwPDB validaton report |
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Full document | 6wpy_full_validation.pdf.gz | 480.9 KB | Display | |
Data in XML | 6wpy_validation.xml.gz | 52.2 KB | Display | |
Data in CIF | 6wpy_validation.cif.gz | 71.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/6wpy ftp://data.pdbj.org/pub/pdb/validation_reports/wp/6wpy | HTTPS FTP |
-Related structure data
Related structure data | 6wpxSC 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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Unit cell |
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-Components
#1: Protein | Mass: 53740.566 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: DW032_06865 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A415J7C9 #2: 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: 1.53 Å3/Da / Density % sol: 19.67 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / Details: 0.1 M MMT pH 5.0 and 25% (w/v) PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4585 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.4585 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→40.49 Å / Num. obs: 23568 / % possible obs: 99.31 % / Redundancy: 6.4 % / CC1/2: 0.94 / Rpim(I) all: 0.197 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 3.6→3.7 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2306 / CC1/2: 0.62 / Rpim(I) all: 0.489 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6WPX Resolution: 3.6→40.49 Å / Cor.coef. Fo:Fc: 0.806 / Cor.coef. Fo:Fc free: 0.764 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.652
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Displacement parameters | Biso max: 181.88 Å2 / Biso mean: 38.11 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.6→40.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.6→3.76 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
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