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- PDB-8avu: Racemic protein crystal structure of aureocin A53 from Staphyloco... -

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Basic information

Entry
Database: PDB / ID: 8avu
TitleRacemic protein crystal structure of aureocin A53 from Staphylococcus aureus in the dimeric state
Components
  • Bacteriocin aureocin A53
  • D-Aureocin A53
KeywordsANTIMICROBIAL PROTEIN / Bacteriocin / D-protein / racemic / mirror-image
Function / homologyBacteriocin 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
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.89 Å
AuthorsLander, A.J. / Baumann, P. / Rizkallah, P. / Jin, Y. / Luk, L.Y.P.
Funding support United Kingdom, 8items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/L027240/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T015799/1 United Kingdom
Leverhulme TrustRPG-2017-195 United Kingdom
Royal SocietyRG170187 United Kingdom
Engineering and Physical Sciences Research Council United Kingdom
Wellcome Trust218568/Z/19/Z United Kingdom
Royal SocietyRG170406 United Kingdom
Wellcome Trust209057/Z/17/Z United Kingdom
CitationJournal: Commun Chem / Year: 2023
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
DepositionAug 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond / pdbx_entry_details
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriocin aureocin A53
B: D-Aureocin A53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,69510
Polymers11,9782
Non-polymers7178
Water2,576143
1
A: Bacteriocin aureocin A53
hetero molecules

A: Bacteriocin aureocin A53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,08614
Polymers11,9882
Non-polymers1,09712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
2
B: D-Aureocin A53
hetero molecules

B: D-Aureocin A53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3056
Polymers11,9682
Non-polymers3364
Water362
TypeNameSymmetry operationNumber
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation2_545-x,y-1,-z1
Buried area1570 Å2
ΔGint-10 kcal/mol
Surface area6760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.560, 23.077, 52.609
Angle α, β, γ (deg.)90.000, 114.351, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Bacteriocin aureocin A53


Mass: 5994.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Staphylococcus aureus (bacteria) / References: UniProt: Q8GPI4
#2: Protein D-Aureocin A53 / Bacteriocin D-Aureocin A53


Mass: 5984.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Staphylococcus aureus (bacteria)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 33.03 %
Crystal growTemperature: 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.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.8153 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8153 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2N8O

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
RfactorNum. reflection% reflection
Rfree0.2105 3106 4.98 %
Rwork0.1938 59261 -
all0.195 --
obs-62367 92.749 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 11.304 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0 Å20.178 Å2
2---0.317 Å20 Å2
3---0.351 Å2
Refinement stepCycle: LAST / Resolution: 0.89→21.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms852 0 47 146 1045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.012945
X-RAY DIFFRACTIONr_bond_other_d0.0020.017972
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.6261259
X-RAY DIFFRACTIONr_angle_other_deg1.1681.5812247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1785108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.56823.57114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.7521586
X-RAY DIFFRACTIONr_chiral_restr0.0950.2104
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021002
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02204
X-RAY DIFFRACTIONr_nbd_refined0.2430.2239
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2140.2907
X-RAY DIFFRACTIONr_nbtor_refined0.2030.2454
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.2400
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2470.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1820.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2430.231
X-RAY DIFFRACTIONr_nbd_other0.2770.2124
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2480.238
X-RAY DIFFRACTIONr_mcbond_it0.850.88420
X-RAY DIFFRACTIONr_mcbond_other0.8450.879420
X-RAY DIFFRACTIONr_mcangle_it1.2031.325526
X-RAY DIFFRACTIONr_mcangle_other1.2021.326527
X-RAY DIFFRACTIONr_scbond_it1.5631.123525
X-RAY DIFFRACTIONr_scbond_other1.5611.123526
X-RAY DIFFRACTIONr_scangle_it1.8141.561731
X-RAY DIFFRACTIONr_scangle_other1.8131.562732
X-RAY DIFFRACTIONr_lrange_it2.63112.8451152
X-RAY DIFFRACTIONr_lrange_other2.6312.8491153
X-RAY DIFFRACTIONr_rigid_bond_restr1.90931917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.89-0.9130.341250.3552290X-RAY DIFFRACTION49.0754
0.913-0.9380.3131630.3162995X-RAY DIFFRACTION65.356
0.938-0.9650.272170.283785X-RAY DIFFRACTION86.1757
0.965-0.9950.2352450.2294305X-RAY DIFFRACTION99.9122
0.995-1.0280.2492170.2144191X-RAY DIFFRACTION99.9773
1.028-1.0640.2212110.1944067X-RAY DIFFRACTION100
1.064-1.1040.2211940.1823921X-RAY DIFFRACTION100
1.104-1.1490.21920.1743797X-RAY DIFFRACTION99.8748
1.149-1.20.1841850.1683595X-RAY DIFFRACTION99.8415
1.2-1.2580.2061750.1693460X-RAY DIFFRACTION100
1.258-1.3260.1761730.1713296X-RAY DIFFRACTION100
1.326-1.4070.2651650.1813114X-RAY DIFFRACTION99.9695
1.407-1.5040.2161490.1832958X-RAY DIFFRACTION99.9678
1.504-1.6240.1941580.1792728X-RAY DIFFRACTION100
1.624-1.7790.1941310.1852548X-RAY DIFFRACTION100
1.779-1.9890.1931150.1892293X-RAY DIFFRACTION100
1.989-2.2960.1831030.1752059X-RAY DIFFRACTION100
2.296-2.810.189780.1931736X-RAY DIFFRACTION99.8899
2.81-3.9670.221690.1881357X-RAY DIFFRACTION99.7901

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