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- PDB-6wi6: Crystal structure of plantacyclin B21AG -

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Basic information

Entry
Database: PDB / ID: 6wi6
TitleCrystal structure of plantacyclin B21AG
ComponentsPlantacyclin B21AG
KeywordsANTIMICROBIAL PROTEIN / Circular bacteriocin / antimicrobial peptide / lactic acid bacteria
Function / homologyMALONATE ION
Function and homology information
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.8 Å
AuthorsSmith, A.T. / Gor, M.C. / Vezina, B. / McMahon, R. / King, G. / Panjikar, S. / Rehm, B. / Martin, J.
Funding support1items
OrganizationGrant numberCountry
Griffith University Postdoctoral Fellowship in Australia
Citation
Journal: Sci Rep / Year: 2020
Title: Crystal structure and site-directed mutagenesis of circular bacteriocin plantacyclin B21AG reveals cationic and aromatic residues important for antimicrobial activity.
Authors: Gor, M.C. / Vezina, B. / McMahon, R.M. / King, G.J. / Panjikar, S. / Rehm, B.H.A. / Martin, J.L. / Smith, A.T.
#1: Journal: Heliyon / Year: 2020
Title: Discovery and characterisation of circular bacteriocin plantacyclin B21AG from Lactiplantibacillus plantarum B21.
Authors: Golneshin, A. / Gor, M.C. / Williamson, N. / Vezina, B. / Van, T.T.H. / May, B.K. / Smith, A.T.
#2: Journal: Plos One / Year: 2020
Title: Cloning and functional expression of a food-grade circular bacteriocin, plantacyclin B21AG, in probiotic Lactobacillus plantarum WCFS1.
Authors: Gor, M.C. / Golneshin, A. / Van, T.T.H. / Moore, R.J. / Smith, A.T.
#3: Journal: Patent / Year: 2016
Title: Bacteriocin polypeptides and uses thereof
Authors: Golneshin, A. / Gor, M.C. / Van, T.T.H. / May, B.K. / Moore, R.J. / Smith, A.T.
History
DepositionApr 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Feb 3, 2021Group: Database references / Category: citation / Item: _citation.details / _citation.pdbx_database_id_patent

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plantacyclin B21AG
B: Plantacyclin B21AG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4813
Polymers11,3792
Non-polymers1021
Water1,00956
1
A: Plantacyclin B21AG


Theoretical massNumber of molelcules
Total (without water)5,6901
Polymers5,6901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Plantacyclin B21AG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,7922
Polymers5,6901
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.131, 93.170, 49.493
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-101-

MLI

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Components

#1: Protein Plantacyclin B21AG


Mass: 5689.649 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lactobacillus plantarum (bacteria) / Strain: B21
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.24 Å3/Da / Density % sol: 44.98 % / Description: Cubic shape
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.1 M sodium malonate, 0.1 M HEPES pH7.0 and 0.5% v/v JED-2003

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→46.58 Å / Num. obs: 9770 / % possible obs: 99.8 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.022 / Rrim(I) all: 0.079 / Net I/σ(I): 15.5 / Num. measured all: 128402
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.8412.30.76270625730.90.2230.7952.496.7
9.01-46.5810.60.034106810110.0120.03635.699.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
ARP/wARPmodel building
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.8→46.58 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.187 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 993 10.2 %RANDOM
Rwork0.1693 ---
obs0.1739 8753 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.42 Å2 / Biso mean: 26.503 Å2 / Biso min: 15.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å2-0 Å2
2---0.42 Å20 Å2
3----0.52 Å2
Refinement stepCycle: final / Resolution: 1.8→46.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms802 0 7 56 865
Biso mean--21.63 39.23 -
Num. residues----116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.019820
X-RAY DIFFRACTIONr_bond_other_d0.0020.02836
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.9591121
X-RAY DIFFRACTIONr_angle_other_deg1.05831909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4375114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.38222.516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.65515118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.947152
X-RAY DIFFRACTIONr_chiral_restr0.1030.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02908
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02158
LS refinement shellResolution: 1.803→1.849 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 62 -
Rwork0.245 637 -
all-699 -
obs--98.45 %

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