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- PDB-5e6n: Crystal structure of C. elegans LGG-2 -

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Basic information

Entry
Database: PDB / ID: 5e6n
TitleCrystal structure of C. elegans LGG-2
ComponentsProtein lgg-2
KeywordsPROTEIN BINDING / ubiquitin-like protein / Atg8 protein family
Function / homology
Function and homology information


PINK1-PRKN Mediated Mitophagy / KEAP1-NFE2L2 pathway / Receptor Mediated Mitophagy / Macroautophagy / cellular response to toxic substance / xenophagy / plasma membrane repair / cellular response to nitrogen starvation / positive regulation of autophagosome maturation / autophagosome maturation ...PINK1-PRKN Mediated Mitophagy / KEAP1-NFE2L2 pathway / Receptor Mediated Mitophagy / Macroautophagy / cellular response to toxic substance / xenophagy / plasma membrane repair / cellular response to nitrogen starvation / positive regulation of autophagosome maturation / autophagosome maturation / autophagosome membrane / autophagosome assembly / autophagosome / macroautophagy / cytoplasmic vesicle / microtubule binding / defense response to Gram-positive bacterium / ubiquitin protein ligase binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 Å
AuthorsQi, X. / Ren, J.Q. / Wu, F. / Zhang, H. / Feng, W.
CitationJournal: Mol.Cell / Year: 2015
Title: Structural Basis of the Differential Function of the Two C. elegans Atg8 Homologs, LGG-1 and LGG-2, in Autophagy
Authors: Wu, F. / Watanabe, Y. / Guo, X.Y. / Qi, X. / Wang, P. / Zhao, H.Y. / Wang, Z. / Fujioka, Y. / Zhang, H. / Ren, J.Q. / Fang, T.C. / Shen, Y.X. / Feng, W. / Hu, J.J. / Noda, N.N. / Zhang, H.
History
DepositionOct 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 6, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein lgg-2
B: Protein lgg-2


Theoretical massNumber of molelcules
Total (without water)27,6982
Polymers27,6982
Non-polymers00
Water1,69394
1
A: Protein lgg-2


Theoretical massNumber of molelcules
Total (without water)13,8491
Polymers13,8491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein lgg-2


Theoretical massNumber of molelcules
Total (without water)13,8491
Polymers13,8491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.254, 24.558, 94.836
Angle α, β, γ (deg.)90.00, 130.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein lgg-2


Mass: 13848.853 Da / Num. of mol.: 2 / Fragment: UNP residues 17-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: lgg-2, ZK593.6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q23536
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 1.98 Å3/Da / Density % sol: 37.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris-HCl, 0.2M Nacl, 25%(w/v) PEG3350 / PH range: 7.8-8.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 12543 / % possible obs: 95.7 % / Redundancy: 5.1 % / Net I/σ(I): 24.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 5.1 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.102→28.307 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.29 / Stereochemistry target values: LS_WUNIT_K1
RfactorNum. reflection% reflection
Rfree0.267 614 4.94 %
Rwork0.2191 --
obs0.2214 12440 94.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.102→28.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1824 0 0 94 1918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091910
X-RAY DIFFRACTIONf_angle_d1.1792578
X-RAY DIFFRACTIONf_dihedral_angle_d17.423775
X-RAY DIFFRACTIONf_chiral_restr0.044275
X-RAY DIFFRACTIONf_plane_restr0.007342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1021-2.31360.33581350.26942936X-RAY DIFFRACTION95
2.3136-2.64820.3191630.25382935X-RAY DIFFRACTION96
2.6482-3.33560.27711550.22762964X-RAY DIFFRACTION95
3.3356-28.30950.22361610.18792991X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: -40.6954 Å / Origin y: 2.708 Å / Origin z: 89.2752 Å
111213212223313233
T0.174 Å2-0.0176 Å2-0.0018 Å2-0.1451 Å20.0263 Å2--0.1531 Å2
L0.8606 °2-0.3854 °2-0.0542 °2-0.5815 °20.1383 °2--0.3252 °2
S-0.0162 Å °0.0094 Å °0.0404 Å °0.0567 Å °0.0102 Å °-0.0815 Å °0.0032 Å °-0.0041 Å °0.0068 Å °
Refinement TLS groupSelection details: all

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