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- PDB-9j5g: Autophagy-related proteins of Magnaporthe oryzae-MoAtg8 -

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Basic information

Entry
Database: PDB / ID: 9j5g
TitleAutophagy-related proteins of Magnaporthe oryzae-MoAtg8
ComponentsAutophagy-related protein
KeywordsAPOPTOSIS / Autophagy-related protein / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


phosphatidylethanolamine binding / fungal-type vacuole membrane / cellular response to nitrogen starvation / autophagosome membrane / macroautophagy / cytoplasmic vesicle / cytosol
Similarity search - Function
Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Autophagy-related protein
Similarity search - Component
Biological speciesPyricularia oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYan, J.Y. / Zhu, X.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of Atg8 at 2.9 Angstroms resolution
Authors: Yan, J.Y. / Zhu, X.M.
History
DepositionAug 12, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Autophagy-related protein


Theoretical massNumber of molelcules
Total (without water)14,4201
Polymers14,4201
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.597, 52.424, 36.443
Angle α, β, γ (deg.)90.000, 114.470, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Autophagy-related protein


Mass: 14419.587 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyricularia oryzae (rice blast fungus) / Gene: PoMZ_10995
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: D4NXH5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.16 Å3/Da / Density % sol: 43.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium acetate trihydrate,20 % w/v PEG 3350,10 % v/v Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.5→26.21 Å / Num. obs: 3341 / % possible obs: 77.01 % / Redundancy: 4.8 % / Biso Wilson estimate: 34.68 Å2 / CC1/2: 0.955 / CC star: 0.989 / Rmerge(I) obs: 0.08688 / Net I/σ(I): 11.77
Reflection shellResolution: 2.5→2.589 Å / Rmerge(I) obs: 0.3454 / Num. unique obs: 352 / CC1/2: 0.995 / CC star: 0.999

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→26.21 Å / SU ML: 0.1773 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.9645
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2512 143 4.29 %
Rwork0.2051 3194 -
obs0.2072 3337 77.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→26.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms924 0 0 10 934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035943
X-RAY DIFFRACTIONf_angle_d0.67291267
X-RAY DIFFRACTIONf_chiral_restr0.0453140
X-RAY DIFFRACTIONf_plane_restr0.0042159
X-RAY DIFFRACTIONf_dihedral_angle_d5.4173124
LS refinement shellResolution: 2.5→2.589 Å
RfactorNum. reflection% reflection
Rfree0.2512 143 -
Rwork0.2051 3194 -
obs--77.1 %
Refinement TLS params.Method: refined / Origin x: 14.0850472693 Å / Origin y: 1.79953241376 Å / Origin z: 9.8312137927 Å
111213212223313233
T0.180635295595 Å20.044756000107 Å20.00534361968104 Å2-0.113118253525 Å2-0.0207516735627 Å2--0.148446537152 Å2
L6.25783391637 °2-0.379928975992 °21.90799722359 °2-2.11264727371 °2-1.00769866012 °2--1.36683778099 °2
S-0.204315079173 Å °-0.35566627073 Å °-0.108534819475 Å °0.204916639914 Å °0.126755897931 Å °-0.0462312355207 Å °0.0129945203952 Å °-0.109523456785 Å °-0.0182515958548 Å °
Refinement TLS groupSelection details: all

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