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- PDB-8fuu: Crystal structure of Xenopus laevis arrestin 1 - P3221 crystal form -

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Basic information

Entry
Database: PDB / ID: 8fuu
TitleCrystal structure of Xenopus laevis arrestin 1 - P3221 crystal form
ComponentsS-arrestin
KeywordsSIGNALING PROTEIN / arrestin 1 / visual arrestin / S-antigen
Function / homology
Function and homology information


G protein-coupled receptor internalization / photoreceptor outer segment / photoreceptor inner segment / visual perception / G protein-coupled receptor binding / signal transduction / membrane
Similarity search - Function
Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / Immunoglobulin E-set
Similarity search - Domain/homology
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsSalom, D. / Barnes, C.L. / Calvert, P.D. / Kiser, P.D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01EY018421 United States
National Institutes of Health/National Eye Institute (NIH/NEI)R01EY028303 United States
Department of Veterans Affairs (VA, United States)I01 BX004939 United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Mechanisms of amphibian arrestin 1 self-association and dynamic distribution in retinal photoreceptors.
Authors: Barnes, C.L. / Salom, D. / Namitz, K.E.W. / Smith, W.C. / Knutson, B.A. / Cosgrove, M.S. / Kiser, P.D. / Calvert, P.D.
History
DepositionJan 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-arrestin


Theoretical massNumber of molelcules
Total (without water)44,6861
Polymers44,6861
Non-polymers00
Water181
1
A: S-arrestin

A: S-arrestin


Theoretical massNumber of molelcules
Total (without water)89,3712
Polymers89,3712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_557x-y,-y,-z+7/31
Buried area2730 Å2
ΔGint-12 kcal/mol
Surface area33040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.773, 80.773, 120.103
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein S-arrestin / Retinal S-antigen / S-AG / Rod photoreceptor arrestin


Mass: 44685.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: sag / Production host: Escherichia coli (E. coli) / References: UniProt: P51477
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% triethylene glycol 100 mM glycine 100 mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.89→50 Å / Num. obs: 10542 / % possible obs: 99.8 % / Redundancy: 9.9 % / CC1/2: 1 / Rmerge(I) obs: 0.049 / Net I/σ(I): 21.53
Reflection shellResolution: 2.89→3.07 Å / Rmerge(I) obs: 2.692 / Mean I/σ(I) obs: 0.77 / Num. unique obs: 1651 / CC1/2: 0.694

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→45.56 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.898 / SU B: 28.648 / SU ML: 0.5 / Cross valid method: THROUGHOUT / ESU R Free: 0.457 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29609 527 5 %RANDOM
Rwork0.24942 ---
obs0.25172 10013 99.85 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 162.748 Å2
Baniso -1Baniso -2Baniso -3
1-3.36 Å21.68 Å20 Å2
2--3.36 Å2-0 Å2
3----10.91 Å2
Refinement stepCycle: 1 / Resolution: 2.89→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2755 0 0 1 2756
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0122813
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162716
X-RAY DIFFRACTIONr_angle_refined_deg0.6081.6513815
X-RAY DIFFRACTIONr_angle_other_deg0.2311.5756294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0765350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg0.221026
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.57210.385506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.9671513
X-RAY DIFFRACTIONr_chiral_restr0.0290.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023111
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02580
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.70716.3551403
X-RAY DIFFRACTIONr_mcbond_other4.70716.3551403
X-RAY DIFFRACTIONr_mcangle_it7.89529.4021752
X-RAY DIFFRACTIONr_mcangle_other7.89329.4031753
X-RAY DIFFRACTIONr_scbond_it4.17616.8561410
X-RAY DIFFRACTIONr_scbond_other4.17616.8531409
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.31230.8822064
X-RAY DIFFRACTIONr_long_range_B_refined12.022151.962832
X-RAY DIFFRACTIONr_long_range_B_other12.02151.962833
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.893→2.968 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.642 37 -
Rwork0.459 713 -
obs--98.55 %

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