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

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Basic information

Entry
Database: PDB / ID: 8avr
TitleRacemic protein crystal structure of aureocin A53 from Staphylococcus aureus in the presence of sulfate
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 / polypeptide(D) / polypeptide(D) (> 10) / Bacteriocin aureocin A53
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 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 1.1Oct 23, 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
C: Bacteriocin aureocin A53
D: D-Aureocin A53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,84315
Polymers23,9574
Non-polymers88711
Water7,350408
1
A: Bacteriocin aureocin A53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2824
Polymers5,9941
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D-Aureocin A53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3005
Polymers5,9841
Non-polymers3164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 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
D: D-Aureocin A53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2044
Polymers5,9841
Non-polymers2203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.740, 36.580, 106.150
Angle α, β, γ (deg.)90.000, 95.980, 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.: 2 / Source method: obtained synthetically / Source: (synth.) Staphylococcus aureus (bacteria) / References: UniProt: Q8GPI4
#2: Protein D-Aureocin A53


Mass: 5984.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Staphylococcus aureus (bacteria)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / Source method: isolated from a natural source / Formula: H2O
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: 2.93 Å3/Da / Density % sol: 58.04 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6
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 sulphate, 0.1 M sodium acetate and 24.5% PEG 4000 v/v precipitant ...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 sulphate, 0.1 M sodium acetate and 24.5% PEG 4000 v/v precipitant condition, pH 5.6 in a 1 microlitre sitting drop. 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: I04-1 / Wavelength: 0.9119 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9119 Å / Relative weight: 1
ReflectionResolution: 1.13→36.2 Å / Num. obs: 89417 / % possible obs: 86 % / Redundancy: 3 % / CC1/2: 0.995 / Net I/σ(I): 9.7
Reflection shellResolution: 1.13→1.15 Å / Redundancy: 1.2 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1958 / CC1/2: 0.787 / % possible all: 38.7

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Processing

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

2n8o


Resolution: 1.13→36.198 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.097 / SU ML: 0.023 / Cross valid method: FREE R-VALUE / ESU R: 0.041 / ESU R Free: 0.041
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.209 4466 4.995 %
Rwork0.1825 84951 -
all0.184 --
obs-89417 85.703 %
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: 14.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.141 Å2-0 Å20.619 Å2
2---0.495 Å20 Å2
3---0.219 Å2
Refinement stepCycle: LAST / Resolution: 1.13→36.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 0 50 417 2171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121812
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171823
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.6242442
X-RAY DIFFRACTIONr_angle_other_deg1.1281.5854203
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9455203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.89223.57128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43115171
X-RAY DIFFRACTIONr_chiral_restr0.080.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021934
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02398
X-RAY DIFFRACTIONr_nbd_refined0.2260.2468
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.21747
X-RAY DIFFRACTIONr_nbtor_refined0.2110.2868
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.2797
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2288
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0080.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2730.219
X-RAY DIFFRACTIONr_nbd_other0.3040.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1430.242
X-RAY DIFFRACTIONr_mcbond_it0.8951.19818
X-RAY DIFFRACTIONr_mcbond_other0.8941.189818
X-RAY DIFFRACTIONr_mcangle_it1.1581.7911016
X-RAY DIFFRACTIONr_mcangle_other1.1571.7911017
X-RAY DIFFRACTIONr_scbond_it1.4421.428994
X-RAY DIFFRACTIONr_scbond_other1.4321.424987
X-RAY DIFFRACTIONr_scangle_it1.7872.0321425
X-RAY DIFFRACTIONr_scangle_other1.772.0241414
X-RAY DIFFRACTIONr_lrange_it2.33817.1812370
X-RAY DIFFRACTIONr_lrange_other2.33917.1882371
X-RAY DIFFRACTIONr_rigid_bond_restr1.02833635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.1590.361560.3542866X-RAY DIFFRACTION39.4414
1.159-1.1910.2411490.2863482X-RAY DIFFRACTION48.6729
1.191-1.2260.2952530.2544843X-RAY DIFFRACTION70.1059
1.226-1.2630.2042900.25949X-RAY DIFFRACTION87.7743
1.263-1.3050.213080.1775920X-RAY DIFFRACTION91.1192
1.305-1.3510.1813090.1615902X-RAY DIFFRACTION93.9211
1.351-1.4020.1652970.1455956X-RAY DIFFRACTION97.021
1.402-1.4590.1613010.1345692X-RAY DIFFRACTION97.813
1.459-1.5240.1692830.1275497X-RAY DIFFRACTION97.9495
1.524-1.5980.1663030.1325221X-RAY DIFFRACTION98.1695
1.598-1.6840.1732550.145044X-RAY DIFFRACTION97.9845
1.684-1.7870.1952460.1454732X-RAY DIFFRACTION97.8958
1.787-1.910.2042600.1554426X-RAY DIFFRACTION97.3815
1.91-2.0630.2112230.174097X-RAY DIFFRACTION96.364
2.063-2.260.171960.1653784X-RAY DIFFRACTION95.8574
2.26-2.5260.2311820.1843314X-RAY DIFFRACTION94.0038
2.526-2.9170.2551630.2032886X-RAY DIFFRACTION91.9204
2.917-3.5720.1991420.2022441X-RAY DIFFRACTION91.889
3.572-5.0480.2241030.2081837X-RAY DIFFRACTION87.9021

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