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- PDB-8sam: Crystal structure of class III lanthipeptide synthetase LP-GS-Thu... -

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Basic information

Entry
Database: PDB / ID: 8sam
TitleCrystal structure of class III lanthipeptide synthetase LP-GS-ThurKC in complex with ATP
ComponentsClass III lanthipeptide, Class III lanthionine synthetase LanKC fusion
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
ADENOSINE-5'-TRIPHOSPHATE / Class III lanthionine synthetase LanKC / Class III lanthipeptide
Similarity search - Component
Biological speciesBacillus thuringiensis serovar andalousiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 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 1.0Oct 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 lanthipeptide, Class III lanthionine synthetase LanKC fusion
B: Class III lanthipeptide, Class III lanthionine synthetase LanKC fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,9086
Polymers205,8142
Non-polymers1,0954
Water7,296405
1
A: Class III lanthipeptide, Class III lanthionine synthetase LanKC fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4543
Polymers102,9071
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Class III lanthipeptide, Class III lanthionine synthetase LanKC fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4543
Polymers102,9071
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.025, 228.659, 84.595
Angle α, β, γ (deg.)90.000, 100.504, 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: ALA / Beg label comp-ID: ALA / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: -29 - 862 / Label seq-ID: 3 - 894

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 lanthipeptide, Class III lanthionine synthetase LanKC fusion


Mass: 102906.969 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, lanKC
Plasmid: pET His6 TEV LIC cloning vector (2B-T) / Details (production host): Addgene plasmid #29666 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U1BAR4, UniProt: A0A6H0TJ16
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.5 Å3/Da / Density % sol: 50.73 % / Description: large plate crystals
Crystal growTemperature: 282.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium citrate tribasic monohydrate and 19 % w/v PEG 3350, protein incubated at 18 mg/mL with 3mM ATP and 3mM Magnesium Chloride and soaked for 6 hours with 7 mM ATP and 7 mM Calcium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.00798 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 25, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00798 Å / Relative weight: 1
ReflectionResolution: 2.15→49.005 Å / Num. obs: 94386 / % possible obs: 86.6 % / Redundancy: 4.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.103 / Net I/σ(I): 9.1
Reflection shellResolution: 2.15→2.157 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.372 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 928 / CC1/2: 0.376 / Rrim(I) all: 1.555 / % possible all: 82.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→49.005 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 9.275 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.23 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2505 4665 4.95 %
Rwork0.203 89583 -
all0.205 --
obs-94248 86.441 %
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: 60.008 Å2
Baniso -1Baniso -2Baniso -3
1--0.855 Å2-0 Å2-0.701 Å2
2--3.844 Å2-0 Å2
3----2.553 Å2
Refinement stepCycle: LAST / Resolution: 2.15→49.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13860 0 64 405 14329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01214192
X-RAY DIFFRACTIONr_angle_refined_deg1.1921.62719161
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80851709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09423.9741
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.202152625
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5091560
X-RAY DIFFRACTIONr_chiral_restr0.0970.21816
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210568
X-RAY DIFFRACTIONr_nbd_refined0.2190.26775
X-RAY DIFFRACTIONr_nbtor_refined0.310.29861
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2695
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.270.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.180.24
X-RAY DIFFRACTIONr_mcbond_it3.9695.8486860
X-RAY DIFFRACTIONr_mcangle_it5.9918.7578561
X-RAY DIFFRACTIONr_scbond_it4.6146.1597332
X-RAY DIFFRACTIONr_scangle_it6.6689.09210600
X-RAY DIFFRACTIONr_lrange_it9.30277.46922003
X-RAY DIFFRACTIONr_ncsr_local_group_10.1310.0527496
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.131250.05009
12BX-RAY DIFFRACTIONLocal ncs0.131250.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.2060.3593520.3596766X-RAY DIFFRACTION88.7089
2.206-2.2660.3542140.3564123X-RAY DIFFRACTION55.087
2.266-2.3320.3373430.3236829X-RAY DIFFRACTION93.8375
2.332-2.4040.3073340.2846595X-RAY DIFFRACTION93.5719
2.404-2.4830.2883130.2566388X-RAY DIFFRACTION92.979
2.483-2.570.293320.2426091X-RAY DIFFRACTION92.3508
2.57-2.6670.2823200.235769X-RAY DIFFRACTION91.303
2.667-2.7750.2782930.2125566X-RAY DIFFRACTION90.8654
2.775-2.8990.2832850.2125237X-RAY DIFFRACTION88.9497
2.899-3.040.282380.2054599X-RAY DIFFRACTION81.8859
3.04-3.2040.272410.2084648X-RAY DIFFRACTION86.6998
3.204-3.3990.2882450.2044596X-RAY DIFFRACTION90.4691
3.399-3.6330.232170.1854252X-RAY DIFFRACTION89.3443
3.633-3.9240.2261980.1763895X-RAY DIFFRACTION88.0973
3.924-4.2980.2241910.173534X-RAY DIFFRACTION86.8501
4.298-4.8040.2031670.1543132X-RAY DIFFRACTION84.2226
4.804-5.5460.2071410.1752618X-RAY DIFFRACTION80.8854
5.546-6.7880.281000.1952143X-RAY DIFFRACTION76.4485
6.788-9.5830.194830.1551831X-RAY DIFFRACTION85.7143
9.583-49.0050.183580.174972X-RAY DIFFRACTION81.0386

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