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- PDB-4j2g: Atg13 HORMA domain -

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Basic information

Entry
Database: PDB / ID: 4j2g
TitleAtg13 HORMA domain
ComponentsKLTH0A00704p
KeywordsUNKNOWN FUNCTION / Autophagy / HORMA / Atg13
Function / homology
Function and homology information


Atg1/ULK1 kinase complex / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / phagophore assembly site / mitophagy / cytosol
Similarity search - Function
Autophagy-related protein 13, N-terminal / Autophagy-related protein 13 / Autophagy-related protein 13 / Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A / HORMA domain / HORMA domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Autophagy-related protein 13
Similarity search - Component
Biological speciesLachancea thermotolerans (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.29 Å
AuthorsJao, C. / Stanley, R.E. / Ragusa, M.J. / Hurley, J.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: A HORMA domain in Atg13 mediates PI 3-kinase recruitment in autophagy.
Authors: Jao, C.C. / Ragusa, M.J. / Stanley, R.E. / Hurley, J.H.
History
DepositionFeb 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Apr 17, 2013Group: Database references / Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KLTH0A00704p
B: KLTH0A00704p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2064
Polymers61,0142
Non-polymers1922
Water1,63991
1
A: KLTH0A00704p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6032
Polymers30,5071
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: KLTH0A00704p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6032
Polymers30,5071
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-11 kcal/mol
Surface area21370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.650, 65.670, 85.760
Angle α, β, γ (deg.)90.00, 101.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein KLTH0A00704p


Mass: 30507.037 Da / Num. of mol.: 2 / Fragment: UNP residues 1-260 / Mutation: L123M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachancea thermotolerans (fungus) / Strain: ATCC 56472 / CBS 6340 / NRRL Y-8284 / Gene: KLTH0A00704g / Production host: Escherichia coli (E. coli) / References: UniProt: C5DB94
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2mM ammonium sulfate, 0.1M MES pH6.5, 20% w/v PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 28, 2012
RadiationMonochromator: filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→84.05 Å / Num. all: 29497 / % possible obs: 99 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 12.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.29→57.25 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.59 / SU B: 6.927 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.21
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26279 1489 5.1 %RANDOM
Rwork0.21445 ---
obs0.21689 27778 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.413 Å2
Baniso -1Baniso -2Baniso -3
1--2.66 Å20 Å2-1.4 Å2
2--6.8 Å20 Å2
3----3.56 Å2
Refinement stepCycle: LAST / Resolution: 2.29→57.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3146 0 10 91 3247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193207
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0521.9954323
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6685378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52923.383133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.16715604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.061526
X-RAY DIFFRACTIONr_chiral_restr0.1310.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212270
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_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: 2.29→2.349 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 105 -
Rwork0.31 2099 -
obs--99.86 %

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