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- PDB-6lwy: Crystal structure of Laterosporulin3, bacteriocin produced by Bre... -

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Basic information

Entry
Database: PDB / ID: 6lwy
TitleCrystal structure of Laterosporulin3, bacteriocin produced by Brevibacillus sp. strain SKR3
ComponentsLaterosporulin3
KeywordsTOXIN / Bacteriocin / Antimicrobial peptide / Laterosporulin / defensin
Function / homologyLaterosporulin defensin-like peptide / Laterosporulin defensin-like peptide / BROMIDE ION / Putative laterosporulin
Function and homology information
Biological speciesBrevibacillus sp. SKR3 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsThakur, K.G. / Solanki, V.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR) India
CitationJournal: To Be Published
Title: Crystal structure of Laterosporulin3, bacteriocin produced by Brevibacillus sp. strain SKR3
Authors: Thakur, K.G. / Solanki, V.
History
DepositionFeb 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Laterosporulin3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9465
Polymers5,6261
Non-polymers3204
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-0 kcal/mol
Surface area3580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.460, 63.460, 63.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-103-

BR

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Components

#1: Protein/peptide Laterosporulin3


Mass: 5626.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brevibacillus sp. SKR3 (bacteria) / Strain: SKR3 / References: UniProt: A0A075R4X6*PLUS
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.89 Å3/Da / Density % sol: 35.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 M potassium bromide, 0.2 M potassium thiocyanate, 0.1 M sodium acetate, 3% w/v PGA-LM (Polyglycolic acid, 200-400 kDa) and 3% w/v PEG (Polyethylene glycol, 20 kDa), pH 5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→36.64 Å / Num. obs: 2214 / % possible obs: 100 % / Redundancy: 14 % / CC1/2: 0.999 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.037 / Rrim(I) all: 0.14 / Rsym value: 0.131 / Net I/σ(I): 16.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.3-2.4214.50.61844923090.8520.0120.0390.0354.5100
7.27-36.6410.30.0359959710.0210.0780.06931.998.9

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
PHENIX1.9refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OZK

4ozk


Resolution: 2.3→36.639 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.81
RfactorNum. reflection% reflection
Rfree0.2331 349 9.45 %
Rwork0.187 --
obs0.1915 2214 100 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 128.61 Å2 / Biso mean: 35.2329 Å2 / Biso min: 13.88 Å2
Refinement stepCycle: final / Resolution: 2.3→36.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms388 0 4 4 396
Biso mean--48.44 21.3 -
Num. residues----49
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID
2.3004-2.89810.29971830.24151669X-RAY DIFFRACTION
2.8981-36.64330.20461660.16451674X-RAY DIFFRACTION
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.4196-2.4658-0.53431.7336-1.75185.283-0.3714-0.52990.7740.47520.30040.2201-0.55470.21970.0830.3069-0.03870.02120.29920.02350.1667-2.808-0.76757.9819
20.5755-0.3419-1.13743.65083.81225.09030.0756-0.16160.22690.0357-0.70770.1903-0.3114-0.13180.20560.2211-0.0537-0.10090.1779-0.00490.28770.6915-7.4631-0.6041
37.65053.2126-2.10881.49-0.85321.045-0.58260.5619-1.2022-0.27240.1920.15760.0989-0.02140.17870.21180.02080.04870.3791-0.12830.5121-12.1209-22.6512-3.9884
42.87252.05271.65143.40410.68651.91680.0008-0.3295-0.55240.4205-0.13520.1560.1238-0.42570.09680.1051-0.00230.02930.34690.01780.3013-4.0748-12.82751.1123
57.66754.87344.08714.58132.25044.11-0.1651-0.186-0.647-0.22640.0089-0.4301-0.5813-0.5281-0.1470.1860.0460.02320.2975-0.12760.2819-6.4319-12.05830.5934
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:8)A2 - 8
2X-RAY DIFFRACTION2chain 'A' and (resseq 9:14)A9 - 14
3X-RAY DIFFRACTION3chain 'A' and (resseq 15:26)A15 - 26
4X-RAY DIFFRACTION4chain 'A' and (resseq 27:34)A27 - 34
5X-RAY DIFFRACTION5chain 'A' and (resseq 35:50)A35 - 50

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