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- PDB-8x8u: Crystal structure of F.occidentalis GABARAP -

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Basic information

Entry
Database: PDB / ID: 8x8u
TitleCrystal structure of F.occidentalis GABARAP
ComponentsGamma-aminobutyric acid receptor-associated protein
KeywordsLIPID BINDING PROTEIN / LIPID TRANSPORT
Function / homology
Function and homology information


GABA receptor binding / autophagy of mitochondrion / cellular response to nitrogen starvation / autophagosome membrane / autophagosome assembly / ubiquitin protein ligase binding / cytosol
Similarity search - Function
Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor-associated protein
Similarity search - Component
Biological speciesFrankliniella occidentalis (western flower thrips)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZhang, S.Q. / Luo, X. / Wu, Z.L. / Zhao, K.H. / Li, X.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32172461 China
CitationJournal: To Be Published
Title: Crystal structure of F.occidentalis GABARAP
Authors: Zhang, S.Q. / Luo, X. / Wu, Z.L. / Zhao, K.H. / Li, X.Y.
History
DepositionNov 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gamma-aminobutyric acid receptor-associated protein


Theoretical massNumber of molelcules
Total (without water)14,0231
Polymers14,0231
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.901, 53.901, 55.665
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Gamma-aminobutyric acid receptor-associated protein


Mass: 14023.142 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Frankliniella occidentalis (western flower thrips)
Gene: LOC113211372 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6J1T1Q2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium acetate, 0.1 M Na citrate tribasic dihydrate pH5.6, 24% w/v Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.6→26.95 Å / Num. obs: 21204 / % possible obs: 99.77 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.019 / Rrim(I) all: 0.068 / Net I/σ(I): 20.3
Reflection shellResolution: 1.6→1.64 Å / Rmerge(I) obs: 1.703 / Num. unique obs: 1380 / Rpim(I) all: 0.565

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIX(1.20.1_4487: ???)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GNU

1gnu


Resolution: 1.6→26.95 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2063 2008 9.47 %
Rwork0.171 --
obs0.1742 21204 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→26.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms991 0 0 88 1079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111018
X-RAY DIFFRACTIONf_angle_d1.1651369
X-RAY DIFFRACTIONf_dihedral_angle_d5.639133
X-RAY DIFFRACTIONf_chiral_restr0.066140
X-RAY DIFFRACTIONf_plane_restr0.012176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.27431330.26521380X-RAY DIFFRACTION99
1.64-1.680.26731510.22581373X-RAY DIFFRACTION100
1.68-1.730.26521430.24861339X-RAY DIFFRACTION100
1.73-1.790.25521510.22051343X-RAY DIFFRACTION100
1.79-1.850.23141440.19631384X-RAY DIFFRACTION100
1.85-1.920.24081520.1671370X-RAY DIFFRACTION100
1.92-2.010.19871440.16921337X-RAY DIFFRACTION100
2.01-2.120.16831370.17061365X-RAY DIFFRACTION100
2.12-2.250.19261460.16981382X-RAY DIFFRACTION100
2.25-2.420.20081330.17871382X-RAY DIFFRACTION100
2.43-2.670.21611450.17311370X-RAY DIFFRACTION100
2.67-3.050.22241420.18731375X-RAY DIFFRACTION100
3.05-3.850.22321460.16511386X-RAY DIFFRACTION100
3.85-26.950.17281410.14931410X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 11.0053 Å / Origin y: 17.7616 Å / Origin z: 26.6962 Å
111213212223313233
T0.2048 Å20.0131 Å2-0.0035 Å2-0.2172 Å2-0.0005 Å2--0.2471 Å2
L2.0573 °20.4523 °2-0.576 °2-2.5775 °2-1.3801 °2--2.1635 °2
S0.0049 Å °-0.0303 Å °-0.1211 Å °-0.0596 Å °0.0784 Å °0.2782 Å °0.0506 Å °-0.1035 Å °-0.0002 Å °
Refinement TLS groupSelection details: all

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