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- PDB-3ruj: Crystal Structure of N-terminal region of yeast Atg7 -

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Basic information

Entry
Database: PDB / ID: 3ruj
TitleCrystal Structure of N-terminal region of yeast Atg7
ComponentsUbiquitin-like modifier-activating enzyme ATG7
KeywordsPROTEIN TRANSPORT / protein binding / Atg3 / Atg10
Function / homology
Function and homology information


Atg12 activating enzyme activity / Atg8 activating enzyme activity / extrinsic component of phagophore assembly site membrane / protein modification by small protein conjugation / C-terminal protein lipidation / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / autophagy of mitochondrion / piecemeal microautophagy of the nucleus ...Atg12 activating enzyme activity / Atg8 activating enzyme activity / extrinsic component of phagophore assembly site membrane / protein modification by small protein conjugation / C-terminal protein lipidation / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / autophagy of mitochondrion / piecemeal microautophagy of the nucleus / cellular response to nitrogen starvation / phagophore assembly site / Neutrophil degranulation / macroautophagy / autophagy / protein transport / mitochondrion / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-like modifier-activating enzyme Atg7 / Ubiquitin-like modifier-activating enzyme Atg7, N-terminal / Ubiquitin-like modifier-activating enzyme Atg7, N-terminal, subdomain 1 / Ubiquitin-like modifier-activating enzyme Atg7, N-terminal, subdomain 2 / Ubiquitin-like modifier-activating enzyme ATG7 N-terminus / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family
Similarity search - Domain/homology
Ubiquitin-like modifier-activating enzyme ATG7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsHong, S.B. / Kim, B.W. / Song, H.K.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Insights into noncanonical E1 enzyme activation from the structure of autophagic E1 Atg7 with Atg8.
Authors: Hong, S.B. / Kim, B.W. / Lee, K.E. / Kim, S.W. / Jeon, H. / Kim, J. / Song, H.K.
History
DepositionMay 5, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-like modifier-activating enzyme ATG7


Theoretical massNumber of molelcules
Total (without water)34,0891
Polymers34,0891
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.846, 112.846, 102.248
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Ubiquitin-like modifier-activating enzyme ATG7 / ATG12-activating enzyme E1 ATG7 / Autophagy-related protein 7 / Cytoplasm to vacuole targeting protein 2


Mass: 34088.559 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP RESIDUES 1-294)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: ATG7, APG7, CVT2, YHR171W / Production host: Escherichia coli (E. coli) / References: UniProt: P38862
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 4.77 Å3/Da / Density % sol: 74.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Na-Hepes pH 8.0, 1.5M LiSO4H2O, 0.01M spermidine tetrahydrochloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1.0, 0.9795, 0.9798, 0.95
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 9, 2010
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97951
30.97981
40.951
ReflectionResolution: 2.1→29.262 Å / Num. all: 37038 / Num. obs: 31750 / % possible obs: 99.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 2.1→2.18 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→29.26 Å / SU ML: 0.29 / σ(F): 0 / Phase error: 26.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2541 1701 5.36 %RANDOM
Rwork0.2278 ---
obs0.2292 31750 85.04 %-
all-37038 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.732 Å2 / ksol: 0.404 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.3038 Å20 Å2-0 Å2
2--3.3038 Å20 Å2
3----6.6075 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 0 155 2490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092388
X-RAY DIFFRACTIONf_angle_d1.3193235
X-RAY DIFFRACTIONf_dihedral_angle_d16.894887
X-RAY DIFFRACTIONf_chiral_restr0.08363
X-RAY DIFFRACTIONf_plane_restr0.005414
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1005-2.16230.35481500.3039262089
2.1623-2.23210.30071280.2924233280
2.2321-2.31180.33961260.2754218874
2.3118-2.40430.30911110.294202070
2.4043-2.51370.30611270.2841212172
2.5137-2.64610.31611330.2819227378
2.6461-2.81180.27011340.2636242182
2.8118-3.02870.27761490.2407269692
3.0287-3.33310.24221660.2267287398
3.3331-3.81450.20911620.202290698
3.8145-4.80240.21151620.1814286297
4.8024-29.26450.27381530.2334273791

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