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- PDB-8avu: 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: 8avu | |||||||||||||||||||||||||||
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Title | Racemic protein crystal structure of aureocin A53 from Staphylococcus aureus in the dimeric state | |||||||||||||||||||||||||||
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![]() | ANTIMICROBIAL PROTEIN / Bacteriocin / D-protein / racemic / mirror-image | |||||||||||||||||||||||||||
Function / homology | Bacteriocin class II, aureocin-like / Aureocin-like type II bacteriocin / killing of cells of another organism / defense response to bacterium / extracellular region / DI(HYDROXYETHYL)ETHER / polypeptide(D) / polypeptide(D) (> 10) / Bacteriocin aureocin A53![]() | |||||||||||||||||||||||||||
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 | ![]() | 59 KB | Display | ![]() |
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PDB format | ![]() | 46.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.1 KB | Display | ![]() |
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Full document | ![]() | 454.6 KB | Display | |
Data in XML | ![]() | 8.8 KB | Display | |
Data in CIF | ![]() | 11.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7p5rC ![]() 8avrC ![]() 8avsC ![]() 8avtC ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 5994.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() | ||||||
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#2: Protein | Mass: 5984.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() | ||||||
#3: Chemical | #4: Chemical | ChemComp-PEG / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.03 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: A racemic mixture of L-Aureocin A53 and D-Aureocin A53 at 40 mg/mL concentration was mixed 1:1 with 0.7 M sodium citrate, 0.1 M Tris precipitant condition, pH 8.5 in a 0.4 microlitre sitting ...Details: A racemic mixture of L-Aureocin A53 and D-Aureocin A53 at 40 mg/mL concentration was mixed 1:1 with 0.7 M sodium citrate, 0.1 M Tris precipitant condition, pH 8.5 in a 0.4 microlitre sitting drop. Crystals were submerged in 2.0 M lithium sulphate 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: 0.8153 Å / Relative weight: 1 |
Reflection | Resolution: 0.89→21.99 Å / Num. obs: 62368 / % possible obs: 92.7 % / Redundancy: 5.9 % / CC1/2: 1 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 0.89→0.91 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1522 / CC1/2: 0.831 / % possible all: 46.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2N8O Resolution: 0.89→21.99 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.78 / SU ML: 0.02 / Cross valid method: FREE R-VALUE / ESU R: 0.026 / ESU R Free: 0.026 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: 11.304 Å2
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Refinement step | Cycle: LAST / Resolution: 0.89→21.99 Å
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Refine LS restraints |
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LS refinement shell |
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