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- PDB-6uak: LahSb - C-terminal methyltransferase involved in RiPP biosynthesis -

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Basic information

Entry
Database: PDB / ID: 6uak
TitleLahSb - C-terminal methyltransferase involved in RiPP biosynthesis
ComponentsSAM dependent methyltransferase LahSB
KeywordsTRANSFERASE / methyltransferase / RiPPs
Function / homology: / Methyltransferase domain / Methyltransferase domain / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase domain-containing protein
Function and homology information
Biological speciesLachnospiraceae bacterium C6A11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsNair, S.K. / Estrada, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Chembiochem / Year: 2020
Title: Characterization of a Dehydratase and Methyltransferase in the Biosynthesis of Ribosomally Synthesized and Post-translationally Modified Peptides in Lachnospiraceae.
Authors: Huo, L. / Zhao, X. / Acedo, J.Z. / Estrada, P. / Nair, S.K. / van der Donk, W.A.
History
DepositionSep 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: SAM dependent methyltransferase LahSB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7072
Polymers35,3221
Non-polymers3841
Water00
1
A: SAM dependent methyltransferase LahSB
hetero molecules

A: SAM dependent methyltransferase LahSB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4134
Polymers70,6442
Non-polymers7692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_764-x+2,-x+y+1,-z-1/31
Buried area3420 Å2
ΔGint-28 kcal/mol
Surface area25220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.729, 115.729, 71.260
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein SAM dependent methyltransferase LahSB


Mass: 35322.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachnospiraceae bacterium C6A11 (bacteria)
Gene: DEO87_04690 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3D0LE54
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
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: 4.06 Å3/Da / Density % sol: 69.68 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium malonate, 16-22% of PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12723 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12723 Å / Relative weight: 1
ReflectionResolution: 2.01→100.2 Å / Num. obs: 34750 / % possible obs: 94.1 % / Redundancy: 20 % / CC1/2: 0.999 / Net I/σ(I): 20.8
Reflection shellResolution: 2.01→2.04 Å / Num. unique obs: 1825 / CC1/2: 0.984

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
pointlessdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.01→25 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.403 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.156
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2768 1680 4.8 %RANDOM
Rwork0.2386 ---
obs0.2404 33046 94.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 142.8 Å2 / Biso mean: 68.566 Å2 / Biso min: 42.67 Å2
Baniso -1Baniso -2Baniso -3
1-3.1 Å21.55 Å20 Å2
2--3.1 Å2-0 Å2
3----10.04 Å2
Refinement stepCycle: final / Resolution: 2.01→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2383 0 26 0 2409
Biso mean--64.31 --
Num. residues----297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022465
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.9783335
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0625295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.52624.561114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.84515430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.9021512
X-RAY DIFFRACTIONr_chiral_restr0.1010.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211856
LS refinement shellResolution: 2.01→2.062 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.244 90 -
Rwork0.209 2217 -
obs--85.04 %

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