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- PDB-8fut: Crystal structure of Xenopus laevis arrestin 1 - P3121 crystal form -

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Basic information

Entry
Database: PDB / ID: 8fut
TitleCrystal structure of Xenopus laevis arrestin 1 - P3121 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 / FOURIER SYNTHESIS / Resolution: 2.54 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
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.830, 81.830, 139.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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.: 22 / 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: 3.02 Å3/Da / Density % sol: 59.27 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 140 mM ammonium chloride 70 mM HEPES, pH 7.5 17.5 % glycerol ethoxylate 6 % glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / 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: 2.54→50 Å / Num. obs: 18443 / % possible obs: 100 % / Redundancy: 20.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.148 / Net I/σ(I): 13.47
Reflection shellResolution: 2.54→2.69 Å / Rmerge(I) obs: 3.361 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2861 / CC1/2: 0.393 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.54→49.73 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 11.847 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.343 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22912 919 5 %RANDOM
Rwork0.18927 ---
obs0.19122 17524 99.97 %-
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 82.753 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0.14 Å2-0 Å2
2---0.28 Å20 Å2
3---0.91 Å2
Refinement stepCycle: 1 / Resolution: 2.54→49.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2874 0 0 22 2896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0122947
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162839
X-RAY DIFFRACTIONr_angle_refined_deg0.921.6523994
X-RAY DIFFRACTIONr_angle_other_deg0.3211.5776583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1865362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg0.8581030
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75810.422533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.3091515
X-RAY DIFFRACTIONr_chiral_restr0.0420.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023259
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02618
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_it3.8598.1031451
X-RAY DIFFRACTIONr_mcbond_other3.8588.1041451
X-RAY DIFFRACTIONr_mcangle_it6.12114.551812
X-RAY DIFFRACTIONr_mcangle_other6.1214.551813
X-RAY DIFFRACTIONr_scbond_it4.6428.6481496
X-RAY DIFFRACTIONr_scbond_other4.648.6491497
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.49915.6842183
X-RAY DIFFRACTIONr_long_range_B_refined10.50182.162990
X-RAY DIFFRACTIONr_long_range_B_other10.582.192986
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.54→2.606 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.597 67 -
Rwork0.515 1273 -
obs--99.93 %

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