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- PDB-8czk: Human LanCL1 bound to GSH and Dhb-Erk peptide -

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Basic information

Entry
Database: PDB / ID: 8czk
TitleHuman LanCL1 bound to GSH and Dhb-Erk peptide
Components
  • Deb-Erk peptide
  • Glutathione S-transferase LANCL1
KeywordsSIGNALING PROTEIN / LanCL1 / lanthipeptide biosynthesis / Erk
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 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
GLUTATHIONE / Glutathione S-transferase LANCL1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 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 1.1Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase LANCL1
B: Glutathione S-transferase LANCL1
C: Deb-Erk peptide
D: Deb-Erk peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1768
Polymers96,4304
Non-polymers7454
Water8,593477
1
A: Glutathione S-transferase LANCL1
C: Deb-Erk peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5884
Polymers48,2152
Non-polymers3732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-51 kcal/mol
Surface area16310 Å2
MethodPISA
2
B: Glutathione S-transferase LANCL1
D: Deb-Erk peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5884
Polymers48,2152
Non-polymers3732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-53 kcal/mol
Surface area16140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.688, 120.562, 144.224
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: Protein/peptide Deb-Erk peptide


Mass: 710.775 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The authors report that chain D displays a better fit to electron density for Try 6 than chain C
Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 7
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: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.91→92.5 Å / Num. obs: 75709 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.041 / Rrim(I) all: 0.126 / Net I/σ(I): 13.5
Reflection shellResolution: 1.914→1.92 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.284 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 809 / CC1/2: 0.785 / Rpim(I) all: 0.438 / Rrim(I) all: 1.36 / % possible all: 100

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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: 1.91→25 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.568 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21338 3759 5 %RANDOM
Rwork0.184 ---
obs0.18542 71871 99.85 %-
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: 31.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2--2.87 Å2-0 Å2
3----3.4 Å2
Refinement stepCycle: 1 / Resolution: 1.91→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6452 0 96 477 7025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0126843
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0791.6369303
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2975844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.25422.291358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.257151105
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7821532
X-RAY DIFFRACTIONr_chiral_restr0.0940.2837
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025346
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_it1.4162.9033287
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1854.3394109
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1153.2263556
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.4840.28210820
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: 1.914→1.963 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 265 -
Rwork0.311 5192 -
obs--99.53 %

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