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- PDB-6sie: Crystal structure of the C-lobe of drosophila Arc 2 -

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Basic information

Entry
Database: PDB / ID: 6sie
TitleCrystal structure of the C-lobe of drosophila Arc 2
ComponentsActivity-regulated cytoskeleton associated protein 2
KeywordsVIRUS LIKE PARTICLE / Arc / Gag homology / atomic resolution / 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 / MOLECULAR REPLACEMENT / Resolution: 2.8 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
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Activity-regulated cytoskeleton associated protein 2
B: Activity-regulated cytoskeleton associated protein 2
C: Activity-regulated cytoskeleton associated protein 2
D: Activity-regulated cytoskeleton associated protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,62810
Polymers42,0524
Non-polymers5766
Water52229
1
A: Activity-regulated cytoskeleton associated protein 2
B: Activity-regulated cytoskeleton associated protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5067
Polymers21,0262
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-76 kcal/mol
Surface area9690 Å2
MethodPISA
2
C: Activity-regulated cytoskeleton associated protein 2
D: Activity-regulated cytoskeleton associated protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1223
Polymers21,0262
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-20 kcal/mol
Surface area9290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.950, 189.950, 40.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

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


Mass: 10512.886 Da / Num. of mol.: 4
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: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.34 Å3/Da / Density % sol: 71.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.25 M ammonium sulphate, 100 mM Tris pH 8.5, 200 mM lithium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 19015 / % possible obs: 99.8 % / Redundancy: 14.3 % / Biso Wilson estimate: 49.8 Å2 / CC1/2: 0.992 / Rrim(I) all: 0.357 / Rsym value: 0.344 / Net I/σ(I): 8.7
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1361 / CC1/2: 0.433 / Rrim(I) all: 3.152 / Rsym value: 3.036 / % possible all: 98.3

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SID

6sid


Resolution: 2.8→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.28 -10 %random
Rwork0.231 ---
obs-18953 99.8 %-
Displacement parametersBiso mean: 50.77 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2838 0 30 29 2897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01322920
X-RAY DIFFRACTIONf_angle_d1.31533921
X-RAY DIFFRACTIONf_chiral_restr0.0661404
X-RAY DIFFRACTIONf_plane_restr0.0086507
X-RAY DIFFRACTIONf_dihedral_angle_d16.91411798

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