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- PDB-3h9d: Crystal Structure of Trypanosoma brucei ATG8 -

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Basic information

Entry
Database: PDB / ID: 3h9d
TitleCrystal Structure of Trypanosoma brucei ATG8
ComponentsMicrotubule-associated protein 1A/1B, light chain 3, putative
KeywordsSTRUCTURAL PROTEIN / autophagy / lipidation / ubiquitin-like / Trypanosoma brucei
Function / homology
Function and homology information


phosphatidylethanolamine binding / phagophore assembly site / cellular response to nitrogen starvation / autophagosome membrane / autophagosome assembly / autophagosome maturation / mitophagy / autophagosome / 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
Autophagy-related protein
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKoopmann, R. / Muhammad, K. / Perbandt, M. / Betzel, C. / Duszenko, M.
CitationJournal: Autophagy / Year: 2009
Title: Trypanosoma brucei ATG8: structural insights into autophagic-like mechanisms in protozoa.
Authors: Koopmann, R. / Muhammad, K. / Perbandt, M. / Betzel, C. / Duszenko, M.
History
DepositionApr 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Microtubule-associated protein 1A/1B, light chain 3, putative
B: Microtubule-associated protein 1A/1B, light chain 3, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4976
Polymers27,3372
Non-polymers1604
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Microtubule-associated protein 1A/1B, light chain 3, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7092
Polymers13,6691
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Microtubule-associated protein 1A/1B, light chain 3, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7894
Polymers13,6691
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.100, 48.600, 127.920
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 Microtubule-associated protein 1A/1B, light chain 3, putative / ATG8


Mass: 13668.503 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Plasmid: PPROEX-HTA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q582K6
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.73 Å3/Da / Density % sol: 55.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 3 uL of the protein solution (8 mg ml-1 protein in 100 mM Tris/HCl buffer, pH 6.5) with 3 uL of precipitating solution (22% v/v PEG 4000, 200 mM ammonia sulfate, 100 mM MES, pH 6.5). ...Details: 3 uL of the protein solution (8 mg ml-1 protein in 100 mM Tris/HCl buffer, pH 6.5) with 3 uL of precipitating solution (22% v/v PEG 4000, 200 mM ammonia sulfate, 100 mM MES, pH 6.5). Droplets were equilibrated against 500 uL of precipitating solution, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorDate: Sep 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 13511

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.873 / SU B: 9.099 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.301 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30959 677 5 %RANDOM
Rwork0.23398 ---
obs0.23773 12834 97.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.085 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.22 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1861 0 4 161 2026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221884
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.9692535
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4145230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.93523.55690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.04915338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0751514
X-RAY DIFFRACTIONr_chiral_restr0.1240.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021418
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1910.2864
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21282
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2136
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.47 41 -
Rwork0.275 876 -
obs--91.98 %

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