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- PDB-6bk9: Crystal Structure of Squid Arrestin -

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Basic information

Entry
Database: PDB / ID: 6bk9
TitleCrystal Structure of Squid Arrestin
ComponentsVisual arrestin
KeywordsSIGNALING PROTEIN / Arrestin / Phosphorylation independent / Squid / invertebrate / Rhodopsin / adapter protein
Function / homology
Function and homology information


signal transduction
Similarity search - Function
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 speciesDoryteuthis pealeii (longfin inshore squid)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.00005573983 Å
AuthorsEger, B.T. / Bandyopadhyay, A. / Yedidi, R.S. / Ernst, O.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Government of CanadaCanada Research Excellence Chair Canada
CitationJournal: J. Mol. Biol. / Year: 2018
Title: A Novel Polar Core and Weakly Fixed C-Tail in Squid Arrestin Provide New Insight into Interaction with Rhodopsin.
Authors: Bandyopadhyay, A. / Van Eps, N. / Eger, B.T. / Rauscher, S. / Yedidi, R.S. / Moroni, T. / West, G.M. / Robinson, K.A. / Griffin, P.R. / Mitchell, J. / Ernst, O.P.
History
DepositionNov 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Visual arrestin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0102
Polymers42,9741
Non-polymers351
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-12 kcal/mol
Surface area14960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.508, 103.508, 153.772
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

#1: Protein Visual arrestin


Mass: 42974.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Doryteuthis pealeii (longfin inshore squid)
Production host: Escherichia coli (E. coli) / References: UniProt: Q963B5
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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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: 2.76 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.2 M Ammonium Sulphate, 300 mM KH2PO4, 100 mM Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.88→31 Å / Num. obs: 11540 / % possible obs: 99.5 % / Redundancy: 10.8 % / Biso Wilson estimate: 92.8591770063 Å2 / CC1/2: 0.995 / Net I/σ(I): 13.9

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JSY

1jsy


Resolution: 3.00005573983→31.0041375064 Å / SU ML: 0.499771948767 / Cross valid method: THROUGHOUT / σ(F): 1.35576831605 / Phase error: 41.0895765951
RfactorNum. reflection% reflection
Rfree0.342251259567 504 4.90129339687 %
Rwork0.292282796384 --
obs0.294736677436 10283 99.9708341435 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 90.8163449963 Å2
Refinement stepCycle: LAST / Resolution: 3.00005573983→31.0041375064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 1 0 2024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008937815964242054
X-RAY DIFFRACTIONf_angle_d1.10956527292795
X-RAY DIFFRACTIONf_chiral_restr0.0498280101948339
X-RAY DIFFRACTIONf_plane_restr0.00700249886769354
X-RAY DIFFRACTIONf_dihedral_angle_d13.77934882991233
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.30170.4075498523351310.285856782372365X-RAY DIFFRACTION100
3.3017-3.77870.2978846480891370.2237124990052379X-RAY DIFFRACTION99.9602701629
3.7787-4.7580.2914101722111120.2625143656632440X-RAY DIFFRACTION100
4.758-31.00580.3742233532911240.3328894962122595X-RAY DIFFRACTION99.9264976112
Refinement TLS params.Method: refined / Origin x: 28.0778725325 Å / Origin y: -19.5949687097 Å / Origin z: -10.2539815501 Å
111213212223313233
T0.706711421133 Å20.100901593015 Å20.118529985715 Å2-0.541912325818 Å2-0.113400091315 Å2--0.454431245546 Å2
L2.89326652314 °2-0.406313799064 °22.17005726773 °2-2.44002611245 °2-1.1775095085 °2--4.55684842911 °2
S0.39063978627 Å °0.391188875551 Å °-0.214853717776 Å °-0.113118418432 Å °0.0689808073417 Å °0.0719788159585 Å °0.198094309501 Å °0.41847419005 Å °-0.353099861515 Å °
Refinement TLS groupSelection details: all

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