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- PDB-3e6u: Crystal structure of Human LanCL1 -

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Basic information

Entry
Database: PDB / ID: 3e6u
TitleCrystal structure of Human LanCL1
ComponentsLanC-like protein 1
KeywordsSIGNALING PROTEIN / Alpha Barrel / Cytoplasm
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 S-transferase LANCL1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsZhang, W. / Zhu, G. / Li, X. / Rao, Z. / Zhang, C.
CitationJournal: Genes Dev. / Year: 2009
Title: Structure of human lanthionine synthetase C-like protein 1 and its interaction with Eps8 and glutathione
Authors: Zhang, W. / Wang, L. / Liu, Y. / Xu, J. / Zhu, G. / Cang, H. / Li, X. / Bartlam, M. / Hensley, K. / Li, G. / Rao, Z. / Zhang, X.C.
History
DepositionAug 16, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LanC-like protein 1
C: LanC-like protein 1
B: LanC-like protein 1
D: LanC-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,8008
Polymers187,5384
Non-polymers2624
Water4,540252
1
A: LanC-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9502
Polymers46,8851
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: LanC-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9502
Polymers46,8851
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: LanC-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9502
Polymers46,8851
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: LanC-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9502
Polymers46,8851
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)194.278, 194.278, 211.829
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
LanC-like protein 1 / 40 kDa erythrocyte membrane protein / p40 / LanCL1


Mass: 46884.621 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LANCL1 / Plasmid: pHAT2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O43813
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 6.189906 Å3/Da / Density % sol: 80.128937 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.5M ammonium formate, 0.1M bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorDate: Nov 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→32.6 Å / Num. obs: 130560 / % possible obs: 92.22 %
Reflection shellResolution: 2.6→2.667 Å / % possible all: 84.22

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→32.58 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 1 / SU B: 11.467 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.285 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27526 5266 4 %RANDOM
Rwork0.24601 ---
obs0.24718 125294 92.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.772 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.6→32.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12972 0 4 252 13228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02213361
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.95718108
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.21851614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19523.56632
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.161152151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3531564
X-RAY DIFFRACTIONr_chiral_restr0.0930.21884
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02110357
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_it0.381.58042
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.707212858
X-RAY DIFFRACTIONr_scbond_it0.66135319
X-RAY DIFFRACTIONr_scangle_it1.0444.55250
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.53 383 -
Rwork0.507 8340 -
obs--84.22 %

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