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- PDB-1wz3: The crystal structure of plant ATG12 -

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Basic information

Entry
Database: PDB / ID: 1wz3
TitleThe crystal structure of plant ATG12
Componentsautophagy 12b
KeywordsPLANT PROTEIN / ubiquitin-fold
Function / homology
Function and homology information


autophagosome assembly / autophagy / protein transport / cytoplasm
Similarity search - Function
Ubiquitin-like protein Atg12 / Ubiquitin-like autophagy protein Apg12 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-like protein ATG12B
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 1.8 Å
AuthorsSuzuki, N.N. / Yoshimoto, K. / Fujioka, Y. / Ohsumi, Y. / Inagaki, F.
CitationJournal: Autophagy / Year: 2005
Title: The crystal structure of plant ATG12 and its biological implication in autophagy.
Authors: Suzuki, N.N. / Yoshimoto, K. / Fujioka, Y. / Ohsumi, Y. / Inagaki, F.
History
DepositionFeb 22, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Category: citation / struct_ref_seq_dif
Item: _citation.pdbx_database_id_DOI / _struct_ref_seq_dif.details
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: autophagy 12b
B: autophagy 12b


Theoretical massNumber of molelcules
Total (without water)21,0462
Polymers21,0462
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-47 kcal/mol
Surface area9450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.693, 38.264, 52.511
Angle α, β, γ (deg.)90.00, 98.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein autophagy 12b / ATG12b / APG12b


Mass: 10522.900 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LVK3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.11 Å3/Da / Density % sol: 41.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: PEG8000, HEPES, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 16031 / Num. obs: 16031 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.8
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.275 / % possible all: 80.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.8→28.92 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 564936.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1528 10 %RANDOM
Rwork0.219 ---
all0.221 15322 --
obs0.221 15322 92.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.9019 Å2 / ksol: 0.403451 e/Å3
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1--5.31 Å20 Å23.46 Å2
2---5.6 Å20 Å2
3---10.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→28.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1285 0 0 156 1441
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.63
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.394 191 9.5 %
Rwork0.334 1825 -
obs-2016 74.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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