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- PDB-6sib: Crystal structure of the domain-swapped N-lobe dimer of drosophil... -

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Basic information

Entry
Database: PDB / ID: 6sib
TitleCrystal structure of the domain-swapped N-lobe dimer of drosophila Arc 2
ComponentsActivity-regulated cytoskeleton associated protein 2
KeywordsVIRUS LIKE PARTICLE / Arc / Gag homology / domain swapping / capsid assembly
Function / homologyTy3 transposon capsid-like protein / Ty3 transposon capsid-like protein / extracellular vesicle / RNA binding / membrane / identical protein binding / Activity-regulated cytoskeleton associated protein 2
Function and homology information
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.9 Å
AuthorsHallin, E.I. / Kursula, P.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway249951 Norway
CitationJournal: Plos One / Year: 2021
Title: Crystal and solution structures reveal oligomerization of individual capsid homology domains of Drosophila Arc.
Authors: Hallin, E.I. / Markusson, S. / Bottger, L. / Torda, A.E. / Bramham, C.R. / Kursula, P.
History
DepositionAug 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 22, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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: Activity-regulated cytoskeleton associated protein 2


Theoretical massNumber of molelcules
Total (without water)8,3741
Polymers8,3741
Non-polymers00
Water28816
1
A: Activity-regulated cytoskeleton associated protein 2

A: Activity-regulated cytoskeleton associated protein 2


Theoretical massNumber of molelcules
Total (without water)16,7492
Polymers16,7492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3520 Å2
ΔGint-42 kcal/mol
Surface area7810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.620, 33.420, 84.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Space group name HallP2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2

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Components

#1: Protein Activity-regulated cytoskeleton associated protein 2 / dArc2


Mass: 8374.413 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Arc2, CG13941 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7JV70
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.09 Å3/Da / Density % sol: 41.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 200 mM ammonium chloride, 100 mM sodium acetate pH 5, 20 % PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 5975 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 40.8 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.111 / Rsym value: 0.103 / Net I/σ(I): 9.9
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1 / Num. unique obs: 417 / CC1/2: 0.395 / Rrim(I) all: 1.568 / Rsym value: 1.432 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
AMPLEphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.9→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.271 -10 %random
Rwork0.238 ---
obs-5952 100 %-
Displacement parametersBiso mean: 43.78 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms527 0 0 16 543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127540
X-RAY DIFFRACTIONf_angle_d1.2298733
X-RAY DIFFRACTIONf_chiral_restr0.051881
X-RAY DIFFRACTIONf_plane_restr0.006492
X-RAY DIFFRACTIONf_dihedral_angle_d13.6358317

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