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- PDB-8avt: Racemic protein crystal structure of aureocin A53 from Staphyloco... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8avt | |||||||||||||||||||||||||||
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Title | Racemic protein crystal structure of aureocin A53 from Staphylococcus aureus in the presence of glycerol 3-phosphate | |||||||||||||||||||||||||||
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Function / homology | ![]() killing of cells of another organism / defense response to bacterium / extracellular region Similarity search - Function | |||||||||||||||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||||||||
![]() | Lander, A.J. / Baumann, P. / Rizkallah, P. / Jin, Y. / Luk, L.Y.P. | |||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Roles of inter- and intramolecular tryptophan interactions in membrane-active proteins revealed by racemic protein crystallography. Authors: Lander, A.J. / Mercado, L.D. / Li, X. / Taily, I.M. / Findlay, B.L. / Jin, Y. / Luk, L.Y.P. | |||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.9 KB | Display | ![]() |
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PDB format | ![]() | 90.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7p5rC ![]() 8avrC ![]() 8avsC ![]() 8avuC ![]() 2n8oS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 4 molecules CDBA
#1: Protein | Mass: 5984.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() #2: Protein | Mass: 5994.228 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 397 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/G3P.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/G3P.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-EDO / ![]() #4: Chemical | ChemComp-PEG / | ![]() #5: Chemical | ![]() #6: Chemical | ChemComp-GOL / | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.32 % |
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Crystal grow![]() | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: A racemic mixture of L-Aureocin A53 and D-Aureocin A53 at 40 mg/mL concentration was mixed 1:1 with 0.2 M ammonium acetate, 0.2 M sodium citrate and 29% PEG 4000 v/v precipitant condition, ...Details: A racemic mixture of L-Aureocin A53 and D-Aureocin A53 at 40 mg/mL concentration was mixed 1:1 with 0.2 M ammonium acetate, 0.2 M sodium citrate and 29% PEG 4000 v/v precipitant condition, pH 5.6 in a 1 microlitre sitting drop. The crystal was soaked with sn-glycerol-3-phosphate (334 mM in the precipitant solution) at 1:1 v/v for 24 hours (50 equivalents). Crystals were submerged in 20% PEG 400 in the precipitant solution as cryoprotectant and flash frozen in liquid nitrogen during harvesting. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 28, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.2→34.531 Å / Num. obs: 96953 / % possible obs: 99.9 % / Redundancy: 13.4 % / CC1/2: 0.999 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4778 / CC1/2: 0.88 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2N8O Resolution: 1.2→34.531 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.555 / SU ML: 0.03 / Cross valid method: FREE R-VALUE / ESU R: 0.037 / ESU R Free: 0.038 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.865 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→34.531 Å
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Refine LS restraints |
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LS refinement shell |
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