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- PDB-8sap: Crystal structure of class III lanthipeptide synthetase ThurKC -

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Basic information

Entry
Database: PDB / ID: 8sap
TitleCrystal structure of class III lanthipeptide synthetase ThurKC
ComponentsClass III lanthionine synthetase LanKC
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 kinase activity / ATP binding / metal ion binding
Similarity search - Function
: / Lanthionine synthetase C-like protein / Lanthionine synthetase C-like / 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
Similarity search - Component
Biological speciesBacillus thuringiensis serovar andalousiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsHernandez Garcia, A. / Nair, S.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)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 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._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

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Assembly

Deposited unit
A: Class III lanthionine synthetase LanKC
B: Class III lanthionine synthetase LanKC


Theoretical massNumber of molelcules
Total (without water)200,0382
Polymers200,0382
Non-polymers00
Water6,918384
1
A: Class III lanthionine synthetase LanKC


Theoretical massNumber of molelcules
Total (without water)100,0191
Polymers100,0191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Class III lanthionine synthetase LanKC


Theoretical massNumber of molelcules
Total (without water)100,0191
Polymers100,0191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.296, 230.230, 84.383
Angle α, β, γ (deg.)90.000, 100.617, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 4 - 863 / Label seq-ID: 7 - 866

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Class III lanthionine synthetase LanKC


Mass: 100018.867 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O

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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: 2.75 Å3/Da / Density % sol: 55.29 % / Description: plates
Crystal growTemperature: 282.15 K / Method: vapor diffusion, sitting drop
Details: 18% (w/v) PEG 3350, 100 mM Bis tris propane/ hydrochloric acid pH 7.5, 200 mM sodium fluoride, and 3% 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12706 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 30, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12706 Å / Relative weight: 1
ReflectionResolution: 2.52→115.115 Å / Num. obs: 68899 / % possible obs: 98.9 % / Redundancy: 4.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.075 / Net I/σ(I): 12.4
Reflection shellResolution: 2.52→2.528 Å / Rmerge(I) obs: 0.824 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 698 / CC1/2: 0.829

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
CRANK2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→115.115 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 11.409 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.578 / ESU R Free: 0.297 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2503 3422 4.967 %
Rwork0.1892 65477 -
all0.192 --
obs-68899 98.889 %
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: 87.984 Å2
Baniso -1Baniso -2Baniso -3
1-3.056 Å20 Å2-1.312 Å2
2--3.1 Å2-0 Å2
3----5.293 Å2
Refinement stepCycle: LAST / Resolution: 2.52→115.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13522 0 0 384 13906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01213787
X-RAY DIFFRACTIONr_angle_refined_deg1.2391.62618601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.09251668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9423.814721
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.603152554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2981559
X-RAY DIFFRACTIONr_chiral_restr0.1090.21758
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210289
X-RAY DIFFRACTIONr_nbd_refined0.2240.26664
X-RAY DIFFRACTIONr_nbtor_refined0.3120.29533
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2662
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2260.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1240.23
X-RAY DIFFRACTIONr_mcbond_it6.1318.6686693
X-RAY DIFFRACTIONr_mcangle_it9.33212.9828354
X-RAY DIFFRACTIONr_scbond_it6.669.0037094
X-RAY DIFFRACTIONr_scangle_it9.9513.35810247
X-RAY DIFFRACTIONr_lrange_it14.335114.64921504
X-RAY DIFFRACTIONr_ncsr_local_group_10.1480.0525536
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.148430.05008
12BX-RAY DIFFRACTIONLocal ncs0.148430.05008
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
2.52-2.5850.382470.31448300.31751030.6350.68399.49050.305
2.585-2.6560.3052510.27247400.27450220.7760.79199.38270.26
2.656-2.7330.2912470.24146190.24449060.8330.8599.18470.226
2.733-2.8170.3372400.23444310.23947130.8170.86499.10880.22
2.817-2.9090.2642120.21443770.21646270.8850.89599.17870.199
2.909-3.0110.272190.20440300.20844010.870.90396.54620.188
3.011-3.1250.2822100.1939700.19443060.8850.91797.07390.175
3.125-3.2520.251960.18539320.18841510.8980.92599.44590.172
3.252-3.3970.281850.1937290.19439360.8880.92499.44110.18
3.397-3.5630.2531860.17835470.18237530.9150.93899.46710.174
3.563-3.7550.2461830.18134070.18436160.9140.94199.2810.179
3.755-3.9830.2361700.18232250.18534170.9290.94399.35620.184
3.983-4.2570.2271420.17130630.17432190.9360.94899.56510.182
4.257-4.5980.2421440.16428280.16829790.9310.9599.7650.179
4.598-5.0360.2491320.16325920.16727420.9170.94799.34350.183
5.036-5.6290.2141310.18522860.18724720.9370.9497.77510.206
5.629-6.4970.261010.20920030.21121900.9150.93296.07310.233
6.497-7.9510.2081030.18217670.18418730.950.9599.83980.216
7.951-11.2180.182810.15113590.15314410.9570.96599.93060.192
11.218-115.1150.358420.2367420.2428060.8750.9297.27050.383

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