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- PDB-1ayr: ARRESTIN FROM BOVINE ROD OUTER SEGMENTS -

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Basic information

Entry
Database: PDB / ID: 1ayr
TitleARRESTIN FROM BOVINE ROD OUTER SEGMENTS
ComponentsARRESTIN
KeywordsSENSORY TRANSDUCTION / ARRESTIN / RHODOPSIN
Function / homology
Function and homology information


opsin binding / Inactivation, recovery and regulation of the phototransduction cascade / G protein-coupled receptor internalization / response to light stimulus / photoreceptor outer segment / photoreceptor inner segment / G protein-coupled receptor binding / phosphoprotein binding / signal transduction / membrane ...opsin binding / Inactivation, recovery and regulation of the phototransduction cascade / G protein-coupled receptor internalization / response to light stimulus / photoreceptor outer segment / photoreceptor inner segment / G protein-coupled receptor binding / phosphoprotein binding / signal transduction / membrane / identical protein binding / cytosol
Similarity search - Function
Immunoglobulin-like - #840 / Immunoglobulin-like - #640 / 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 ...Immunoglobulin-like - #840 / Immunoglobulin-like - #640 / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.3 Å
AuthorsGranzin, J. / Wilden, U. / Choe, H.-W. / Labahn, J. / Krafft, B. / Bueldt, G.
Citation
Journal: Nature / Year: 1998
Title: X-ray crystal structure of arrestin from bovine rod outer segments.
Authors: Granzin, J. / Wilden, U. / Choe, H.W. / Labahn, J. / Krafft, B. / Buldt, G.
#1: Journal: FEBS Lett. / Year: 1997
Title: Crystallization and Preliminary X-Ray Analysis of Arrestin from Bovine Rod Outer Segment
Authors: Wilden, U. / Choe, H.W. / Krafft, B. / Granzin, J.
History
DepositionNov 10, 1997Processing site: BNL
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ARRESTIN
B: ARRESTIN
C: ARRESTIN
D: ARRESTIN


Theoretical massNumber of molelcules
Total (without water)164,0054
Polymers164,0054
Non-polymers00
Water5,134285
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.170, 185.530, 90.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.39485, 0.91404, 0.09288), (-0.57888, -0.32601, 0.7474), (0.71343, 0.24135, 0.65785)33.61734, 89.38696, -71.57841
2given(0.09309, -0.99466, 0.04465), (-0.99478, -0.09104, 0.04606), (-0.04175, -0.04871, -0.99794)74.68359, 84.44318, 28.17106
3given(0.58001, 0.36599, -0.72776), (0.40692, -0.90411, -0.13037), (-0.70569, -0.22052, -0.67333)-11.23432, 45.66153, 93.59536

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Components

#1: Protein
ARRESTIN / / RETINAL S-ANTIGEN / 48 KD PROTEIN


Mass: 41001.273 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Cell: ROD OUTER SEGMENTS / Cellular location: CYTOPLASM / Organ: EYE / Tissue: RETINA / References: UniProt: P08168
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O
Compound detailsARRESTIN QUENCHES THE LIGHT-INDUCED ENZYME CASCADE, BINDS TO PHOSPHORYLATED LIGHT-ACTIVATED RHODOPSIN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.94 Å3/Da / Density % sol: 68.5 %
Crystal growpH: 7.2 / Details: pH 7.2
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
136 mg/mlprotein1drop
218 mMPIPES1drop
30.5 M1dropKCl
430 %ethylene glycol1drop
58 %PEG60001drop
618 %PEG2001drop
76 %PEG10001drop
840 mMPIPES1reservoir
90.6 M1reservoirKCl
100.02 %ethylene glycol1reservoir
115.7 %PEG60001reservoir
1213 %PEG2001reservoir
134 %PEG10001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1996 / Details: PT COATED TORROIDAL MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→26.976 Å / Num. obs: 478820 / % possible obs: 95.1 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.075 / Rsym value: 0.172 / Net I/σ(I): 8.6
Reflection shellResolution: 3.3→3.39 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 4.3 / Rsym value: 0.172 / % possible all: 79.7
Reflection shell
*PLUS
% possible obs: 79.7 %

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
CCP4(SCALA)data scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MIRAS / Resolution: 3.3→130 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUPED, UNRESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: TORSION-ANGLE MOLECULAR DYNAMICS SLOW COOL REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.316 1660 5 %RANDOM
Rwork0.254 ---
obs0.254 41556 95.1 %-
Displacement parametersBiso mean: 27.71 Å2
Baniso -1Baniso -2Baniso -3
1--55.139 Å20 Å20 Å2
2---61.582 Å20 Å2
3----31.13 Å2
Refinement stepCycle: LAST / Resolution: 3.3→130 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11460 0 0 285 11745
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: CONSTRAINTS + RESTRAINTS
LS refinement shellResolution: 3.3→3.45 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.316 146 2.8 %
Rwork0.254 4153 -
obs--76.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.254

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