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

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Basic information

Entry
Database: PDB / ID: 8avt
TitleRacemic protein crystal structure of aureocin A53 from Staphylococcus aureus in the presence of glycerol 3-phosphate
Components
  • Bacteriocin aureocin A53
  • D-Aureocin A53
KeywordsANTIMICROBIAL PROTEIN / Bacteriocin / D-protein / racemic / mirror-image
Function / homology
Function and homology information


killing of cells of another organism / defense response to bacterium / extracellular region
Similarity search - Function
Bacteriocin class II, aureocin-like / Aureocin-like type II bacteriocin
Similarity search - Domain/homology
SN-GLYCEROL-3-PHOSPHATE / DI(HYDROXYETHYL)ETHER / polypeptide(D) / polypeptide(D) (> 10) / Bacteriocin aureocin A53
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 Council2107414 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 6, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,80913
Polymers23,9574
Non-polymers8539
Water6,990388
1
C: D-Aureocin A53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2144
Polymers5,9841
Non-polymers2303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: D-Aureocin A53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2804
Polymers5,9841
Non-polymers2963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Bacteriocin aureocin A53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0562
Polymers5,9941
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Bacteriocin aureocin A53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2583
Polymers5,9941
Non-polymers2642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.718, 37.239, 114.088
Angle α, β, γ (deg.)90.000, 92.973, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 4 molecules CDBA

#1: Protein D-Aureocin A53 / Bacteriocin D-Aureocin A53


Mass: 5984.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Staphylococcus aureus (bacteria)
#2: Protein Bacteriocin aureocin A53


Mass: 5994.228 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Staphylococcus aureus (bacteria) / References: UniProt: Q8GPI4

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Non-polymers , 5 types, 397 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-G3P / SN-GLYCEROL-3-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H9O6P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.26 Å3/Da / Density % sol: 62.32 %
Crystal growTemperature: 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.

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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: 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 shellResolution: 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

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

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
RfactorNum. reflection% reflection
Rfree0.2033 4912 5.067 %
Rwork0.176 92035 -
all0.177 --
obs-96947 99.866 %
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: 19.865 Å2
Baniso -1Baniso -2Baniso -3
1--0.065 Å2-0 Å20.108 Å2
2--0.923 Å20 Å2
3----0.864 Å2
Refinement stepCycle: LAST / Resolution: 1.2→34.531 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 0 53 396 2153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121825
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171853
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.6262452
X-RAY DIFFRACTIONr_angle_other_deg1.1881.5864278
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8165205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.92523.79329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0115174
X-RAY DIFFRACTIONr_chiral_restr0.1030.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021950
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02402
X-RAY DIFFRACTIONr_nbd_refined0.2390.2479
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.21675
X-RAY DIFFRACTIONr_nbtor_refined0.2030.2880
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.2757
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2224
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1340.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2470.216
X-RAY DIFFRACTIONr_nbd_other0.380.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1610.227
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0260.21
X-RAY DIFFRACTIONr_mcbond_it1.6371.591824
X-RAY DIFFRACTIONr_mcbond_other1.6381.591823
X-RAY DIFFRACTIONr_mcangle_it1.752.3891026
X-RAY DIFFRACTIONr_mcangle_other1.7492.3891027
X-RAY DIFFRACTIONr_scbond_it2.7171.941999
X-RAY DIFFRACTIONr_scbond_other2.6261.935996
X-RAY DIFFRACTIONr_scangle_it3.0322.7371424
X-RAY DIFFRACTIONr_scangle_other3.0312.7391425
X-RAY DIFFRACTIONr_lrange_it3.32622.8262343
X-RAY DIFFRACTIONr_lrange_other3.05321.62226
X-RAY DIFFRACTIONr_rigid_bond_restr2.81833674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.2310.3013620.3196723X-RAY DIFFRACTION99.4945
1.231-1.2650.3273440.2886596X-RAY DIFFRACTION99.6554
1.265-1.3020.2773350.2516386X-RAY DIFFRACTION99.7033
1.302-1.3420.2513420.2226245X-RAY DIFFRACTION99.7577
1.342-1.3860.2073230.1896019X-RAY DIFFRACTION99.8111
1.386-1.4340.2023170.1695888X-RAY DIFFRACTION99.8873
1.434-1.4880.1843000.1475623X-RAY DIFFRACTION99.8988
1.488-1.5490.172880.1345429X-RAY DIFFRACTION99.9825
1.549-1.6180.1862840.1355235X-RAY DIFFRACTION100
1.618-1.6970.1782620.1314998X-RAY DIFFRACTION100
1.697-1.7890.1942740.134760X-RAY DIFFRACTION100
1.789-1.8970.1882610.1354448X-RAY DIFFRACTION100
1.897-2.0280.1962150.1524265X-RAY DIFFRACTION100
2.028-2.1910.1951950.1543984X-RAY DIFFRACTION99.9761
2.191-2.40.1951910.1493622X-RAY DIFFRACTION100
2.4-2.6830.2051620.1623332X-RAY DIFFRACTION100
2.683-3.0970.2151740.1842915X-RAY DIFFRACTION100
3.097-3.7930.1991280.1772500X-RAY DIFFRACTION100
3.793-5.3610.1821100.21941X-RAY DIFFRACTION100

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