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- PDB-5azh: Crystal structure of LGG-2 fused with an EEEWEEL peptide -

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Basic information

Entry
Database: PDB / ID: 5azh
TitleCrystal structure of LGG-2 fused with an EEEWEEL peptide
ComponentsEEEWEEL peptide,Protein lgg-2
KeywordsPROTEIN BINDING / autophagy / ubiquitin-like
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 speciessynthetic construct (others)
Caenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWatanabe, Y. / Fujioka, Y. / Noda, N.N.
Funding support Japan, 3items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology of Japan25111004 Japan
Ministry of Education, Culture, Sports, Science and Technology of Japan26870828 Japan
Japan Science and Technology AgencyCREST Japan
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 5, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EEEWEEL peptide,Protein lgg-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1172
Polymers15,0931
Non-polymers241
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-5 kcal/mol
Surface area8610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.532, 55.193, 72.592
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 EEEWEEL peptide,Protein lgg-2


Mass: 15093.157 Da / Num. of mol.: 1 / Fragment: UNP residues 11-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others), (gene. exp.) Caenorhabditis elegans (invertebrata)
Plasmid: pGEX-6P / Gene: lgg-2 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q23536
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: sodium chloride, magnesium chloride, HEPES

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Sep 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→43.94 Å / Num. obs: 7374 / % possible obs: 98.3 % / Redundancy: 18.4 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 29.3
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.859 / % possible all: 85.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→43.94 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.909 / SU B: 22.918 / SU ML: 0.271 / Cross valid method: THROUGHOUT / ESU R: 0.397 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28827 341 5.1 %RANDOM
Rwork0.23564 ---
obs0.23826 6372 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.276 Å2
Baniso -1Baniso -2Baniso -3
1--4.01 Å2-0 Å2-0 Å2
2---2.6 Å20 Å2
3---6.6 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1038 0 1 35 1074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191062
X-RAY DIFFRACTIONr_bond_other_d0.0020.02998
X-RAY DIFFRACTIONr_angle_refined_deg1.2451.9641434
X-RAY DIFFRACTIONr_angle_other_deg0.91932298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4645126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39223.50957
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.7815188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8921511
X-RAY DIFFRACTIONr_chiral_restr0.070.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211206
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02255
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_it0.9723.94507
X-RAY DIFFRACTIONr_mcbond_other0.9733.941506
X-RAY DIFFRACTIONr_mcangle_it1.6875.907632
X-RAY DIFFRACTIONr_mcangle_other1.6865.905633
X-RAY DIFFRACTIONr_scbond_it1.0244.109555
X-RAY DIFFRACTIONr_scbond_other1.0244.11555
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7596.09802
X-RAY DIFFRACTIONr_long_range_B_refined4.83336.8494114
X-RAY DIFFRACTIONr_long_range_B_other4.76436.7934079
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 17 -
Rwork0.293 447 -
obs--94.31 %
Refinement TLS params.Method: refined / Origin x: -7.266 Å / Origin y: -2.612 Å / Origin z: 10.205 Å
111213212223313233
T0.125 Å2-0.008 Å2-0.0465 Å2-0.1401 Å2-0 Å2--0.0381 Å2
L5.9592 °20.5109 °20.6012 °2-1.8309 °2-0.2667 °2--0.8833 °2
S-0.2571 Å °-0.0543 Å °0.4073 Å °-0.2836 Å °0.2128 Å °0.0775 Å °0.1175 Å °0.0602 Å °0.0444 Å °

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