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- PDB-8sao: Crystal structure of class III lanthipeptide synthetase ThurKC in... -

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Basic information

Entry
Database: PDB / ID: 8sao
TitleCrystal structure of class III lanthipeptide synthetase ThurKC in complex with ThurA1 leader peptide
Components
  • Class III lanthionine synthetase LanKC
  • Class III lanthipeptide
KeywordsBIOSYNTHETIC PROTEIN / lanthipeptide / synthetase / kinase / lyase / cyclase / complex / class III / RIPP / natural product / transferase / bacterial / labionin
Function / homology
Function and homology information


peptide modification / protein serine/threonine kinase activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Lanthionine synthetase C-like / Lanthionine synthetase C-like protein / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Class III lanthionine synthetase LanKC / Class III lanthipeptide
Similarity search - Component
Biological speciesBacillus thuringiensis serovar andalousiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.502 Å
AuthorsHernandez Garcia, A. / Nair, S.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM079038 United States
CitationJournal: Acs Cent.Sci. / Year: 2023
Title: Structure and Function of a Class III Metal-Independent Lanthipeptide Synthetase.
Authors: Hernandez Garcia, A. / Nair, S.K.
History
DepositionApr 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_CSD / _citation.journal_volume ..._citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Class III lanthipeptide
C: Class III lanthipeptide
B: Class III lanthionine synthetase LanKC
D: Class III lanthionine synthetase LanKC


Theoretical massNumber of molelcules
Total (without water)199,9664
Polymers199,9664
Non-polymers00
Water00
1
A: Class III lanthipeptide
B: Class III lanthionine synthetase LanKC


Theoretical massNumber of molelcules
Total (without water)99,9832
Polymers99,9832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-9 kcal/mol
Surface area36100 Å2
MethodPISA
2
C: Class III lanthipeptide
D: Class III lanthionine synthetase LanKC


Theoretical massNumber of molelcules
Total (without water)99,9832
Polymers99,9832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-9 kcal/mol
Surface area36320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.028, 52.899, 233.417
Angle α, β, γ (deg.)90.000, 95.728, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
32B
42D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAASPASPAA-29 - -161 - 14
221ALAALAASPASPCB-29 - -161 - 14
332ASNASNVALVALBC4 - 8621 - 859
442ASNASNVALVALDD4 - 8621 - 859

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4

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Components

#1: Protein/peptide Class III lanthipeptide


Mass: 1584.834 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis serovar andalousiensis (bacteria)
Gene: EVG22_32215, EVG22_32220, EVG22_32230, EVG22_32235, EVG22_32240
Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U1BAR4
#2: Protein Class III lanthionine synthetase LanKC


Mass: 98398.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis serovar andalousiensis (bacteria)
Gene: lanKC / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6H0TJ16

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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: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growTemperature: 282.15 K / Method: vapor diffusion, hanging drop
Details: 15% glycerol, 16% PEG 6000, 80 mM sodium cacodylate pH 6.5, 160 mM calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.00385 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 8, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00385 Å / Relative weight: 1
ReflectionResolution: 2.5→232.3 Å / Num. obs: 66801 / % possible obs: 96.9 % / Redundancy: 4.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.104 / Net I/σ(I): 9.8
Reflection shellResolution: 2.5→2.51 Å / Rmerge(I) obs: 0.519 / Num. unique obs: 524 / CC1/2: 0.727

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.502→232.252 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.861 / SU B: 14.757 / SU ML: 0.326 / Cross valid method: FREE R-VALUE / ESU R: 0.826 / ESU R Free: 0.369 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.3072 3260 4.88 %
Rwork0.2456 63540 -
all0.249 --
obs-66800 96.909 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 62.608 Å2
Baniso -1Baniso -2Baniso -3
1--5.611 Å20 Å2-0.241 Å2
2--2.175 Å2-0 Å2
3---3.415 Å2
Refinement stepCycle: LAST / Resolution: 2.502→232.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13859 0 0 0 13859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01214125
X-RAY DIFFRACTIONr_angle_refined_deg1.2421.62619057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.92451710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24423.9741
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.672152620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5451560
X-RAY DIFFRACTIONr_chiral_restr0.1140.21806
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210538
X-RAY DIFFRACTIONr_nbd_refined0.2540.26823
X-RAY DIFFRACTIONr_nbtor_refined0.3160.29609
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2438
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2480.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1840.21
X-RAY DIFFRACTIONr_mcbond_it4.0116.1656864
X-RAY DIFFRACTIONr_mcangle_it6.4659.2368566
X-RAY DIFFRACTIONr_scbond_it3.9256.337261
X-RAY DIFFRACTIONr_scangle_it6.1079.40210491
X-RAY DIFFRACTIONr_lrange_it10.27181.89421563
X-RAY DIFFRACTIONr_ncsr_local_group_10.2960.05272
X-RAY DIFFRACTIONr_ncsr_local_group_20.1450.0526369
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.296380.05004
12CX-RAY DIFFRACTIONLocal ncs0.296380.05004
23BX-RAY DIFFRACTIONLocal ncs0.144520.05009
24DX-RAY DIFFRACTIONLocal ncs0.144520.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.502-2.5670.3912150.35537170.35750170.6630.68478.37350.35
2.567-2.6370.3642080.30143430.30449560.7570.76991.82810.289
2.637-2.7140.3582340.29144620.29447650.7750.80998.55190.279
2.714-2.7970.3382200.28144670.28446970.8150.81899.78710.269
2.797-2.8890.3552290.27742260.28144780.7880.82799.48640.262
2.889-2.990.3171990.25741620.2643720.8320.85599.74840.243
2.99-3.1030.3281890.25140680.25442830.8380.86599.3930.242
3.103-3.230.3371870.24837940.25240090.8460.87299.30160.24
3.23-3.3740.351850.25637100.26139120.8270.86599.56540.253
3.374-3.5380.3121890.25635390.25837430.8420.87599.59930.254
3.538-3.730.3231610.25732640.2635490.8530.88196.50610.263
3.73-3.9560.3271390.24631230.24933480.8570.88597.43130.256
3.956-4.2290.2821720.23129960.23331710.8750.90899.90540.247
4.229-4.5670.2581560.21928140.22129770.9070.92499.76490.241
4.567-5.0030.2611360.21425880.21727350.9060.91999.59780.242
5.003-5.5930.2841350.23223270.23524710.8850.90599.63580.263
5.593-6.4580.3041120.26220900.26422230.8690.89899.05530.295
6.458-7.9080.279910.20616500.2118720.9060.93393.00210.24
7.908-11.1770.225670.17814070.18114860.930.94499.19250.223
11.177-232.2520.426360.2767930.2828670.8040.88895.61710.427

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