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Yorodumi- PDB-6lwy: Crystal structure of Laterosporulin3, bacteriocin produced by Bre... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lwy | ||||||
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Title | Crystal structure of Laterosporulin3, bacteriocin produced by Brevibacillus sp. strain SKR3 | ||||||
Components | Laterosporulin3 | ||||||
Keywords | TOXIN / Bacteriocin / Antimicrobial peptide / Laterosporulin / defensin | ||||||
Function / homology | Laterosporulin defensin-like peptide / Laterosporulin defensin-like peptide / BROMIDE ION / Putative laterosporulin Function and homology information | ||||||
Biological species | Brevibacillus sp. SKR3 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Thakur, K.G. / Solanki, V. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Laterosporulin3, bacteriocin produced by Brevibacillus sp. strain SKR3 Authors: Thakur, K.G. / Solanki, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lwy.cif.gz | 34.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lwy.ent.gz | 21.9 KB | Display | PDB format |
PDBx/mmJSON format | 6lwy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/6lwy ftp://data.pdbj.org/pub/pdb/validation_reports/lw/6lwy | HTTPS FTP |
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-Related structure data
Related structure data | 4ozkS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 5626.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brevibacillus sp. SKR3 (bacteria) / Strain: SKR3 / References: UniProt: A0A075R4X6*PLUS | ||||
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#2: Chemical | ChemComp-BR / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 35.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.2 M potassium bromide, 0.2 M potassium thiocyanate, 0.1 M sodium acetate, 3% w/v PGA-LM (Polyglycolic acid, 200-400 kDa) and 3% w/v PEG (Polyethylene glycol, 20 kDa), pH 5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 9, 2014 | |||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→36.64 Å / Num. obs: 2214 / % possible obs: 100 % / Redundancy: 14 % / CC1/2: 0.999 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.037 / Rrim(I) all: 0.14 / Rsym value: 0.131 / Net I/σ(I): 16.6 | |||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OZK Resolution: 2.3→36.639 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.81
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 128.61 Å2 / Biso mean: 35.2329 Å2 / Biso min: 13.88 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→36.639 Å
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LS refinement shell |
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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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