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- PDB-8czl: Human LanCL1 bound to methyl glutathione (MeGSH) -

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Basic information

Entry
Database: PDB / ID: 8czl
TitleHuman LanCL1 bound to methyl glutathione (MeGSH)
ComponentsGlutathione S-transferase LANCL1
KeywordsSIGNALING PROTEIN / LanCL1 / lanthibiotic cyclase
Function / homology
Function and homology information


peptide modification / glutathione binding / cellular detoxification / low-density lipoprotein particle receptor binding / glutathione transferase / glutathione transferase activity / G protein-coupled receptor activity / SH3 domain binding / carbohydrate metabolic process / G protein-coupled receptor signaling pathway ...peptide modification / glutathione binding / cellular detoxification / low-density lipoprotein particle receptor binding / glutathione transferase / glutathione transferase activity / G protein-coupled receptor activity / SH3 domain binding / carbohydrate metabolic process / G protein-coupled receptor signaling pathway / zinc ion binding / plasma membrane / cytoplasm
Similarity search - Function
LanC-like protein, eukaryotic / Lanthionine synthetase C-like protein / Lanthionine synthetase C-like protein / Lanthionine synthetase C-like / Six-hairpin glycosidase-like superfamily
Similarity search - Domain/homology
L-GAMMA-GLUTAMYL-S-METHYLCYSTEINYLGLYCINE / Glutathione S-transferase LANCL1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsOngpipattanakul, C. / 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: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: The mechanism of thia-Michael addition catalyzed by LanC enzymes.
Authors: Ongpipattanakul, C. / Liu, S. / Luo, Y. / Nair, S.K. / van der Donk, W.A.
History
DepositionMay 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S-transferase LANCL1
B: Glutathione S-transferase LANCL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,7826
Polymers95,0092
Non-polymers7744
Water11,818656
1
A: Glutathione S-transferase LANCL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8913
Polymers47,5041
Non-polymers3872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutathione S-transferase LANCL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8913
Polymers47,5041
Non-polymers3872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.485, 120.909, 143.102
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glutathione S-transferase LANCL1 / 40 kDa erythrocyte membrane protein / p40 / LanC-like protein 1


Mass: 47504.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LANCL1, GPR69A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O43813, glutathione transferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GSM / L-GAMMA-GLUTAMYL-S-METHYLCYSTEINYLGLYCINE / S-METHYL-GLUTATHIONE


Mass: 321.350 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H19N3O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 656 / 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: 2.64 Å3/Da / Density % sol: 53.39 % / Description: Rods
Crystal growTemperature: 282.15 K / Method: vapor diffusion, hanging drop
Details: 0.70-0.75 M succinic acid pH 7.0, 0.1 M bis-tris-propane pH 7.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.577→92.357 Å / Num. obs: 130838 / % possible obs: 98.3 % / Redundancy: 9.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.029 / Rrim(I) all: 0.088 / Net I/σ(I): 17.1
Reflection shellResolution: 1.577→1.605 Å / Rmerge(I) obs: 0.959 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6255 / CC1/2: 0.8 / Rpim(I) all: 0.348 / Rrim(I) all: 1.023

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
AutoProcessdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E6U

3e6u


Resolution: 1.58→25 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.613 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20388 6438 4.9 %RANDOM
Rwork0.18114 ---
obs0.18226 123816 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2--1.72 Å2-0 Å2
3----1.04 Å2
Refinement stepCycle: 1 / Resolution: 1.58→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6406 0 44 656 7106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0126756
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0691.6359198
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3385842
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.2222.273352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.931151097
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7621532
X-RAY DIFFRACTIONr_chiral_restr0.0910.2831
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025272
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9631.9243248
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6222.8844070
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5052.1613508
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.49827.36710990
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 504 -
Rwork0.269 8784 -
obs--96.37 %

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