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- PDB-1cf1: ARRESTIN FROM BOVINE ROD OUTER SEGMENTS -

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Basic information

Entry
Database: PDB / ID: 1cf1
TitleARRESTIN FROM BOVINE ROD OUTER SEGMENTS
ComponentsPROTEIN (ARRESTIN)
KeywordsSTRUCTURAL PROTEIN / VISUAL ARRESTIN / DESENSITISATION OF THE VISUAL TRANSDUCTION CASCADE / BINDING TO ACTICATED AND PHOSPHORYLATED 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: 2.8 Å
AuthorsHirsch, J.A. / Schubert, C. / Gurevich, V.V. / Sigler, P.B.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: The 2.8 A crystal structure of visual arrestin: a model for arrestin's regulation.
Authors: Hirsch, J.A. / Schubert, C. / Gurevich, V.V. / Sigler, P.B.
History
DepositionMar 23, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ARRESTIN)
B: PROTEIN (ARRESTIN)
C: PROTEIN (ARRESTIN)
D: PROTEIN (ARRESTIN)


Theoretical massNumber of molelcules
Total (without water)181,0434
Polymers181,0434
Non-polymers00
Water45025
1
A: PROTEIN (ARRESTIN)


Theoretical massNumber of molelcules
Total (without water)45,2611
Polymers45,2611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN (ARRESTIN)


Theoretical massNumber of molelcules
Total (without water)45,2611
Polymers45,2611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PROTEIN (ARRESTIN)


Theoretical massNumber of molelcules
Total (without water)45,2611
Polymers45,2611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PROTEIN (ARRESTIN)


Theoretical massNumber of molelcules
Total (without water)45,2611
Polymers45,2611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: PROTEIN (ARRESTIN)

D: PROTEIN (ARRESTIN)


Theoretical massNumber of molelcules
Total (without water)90,5212
Polymers90,5212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
Buried area2200 Å2
ΔGint-5 kcal/mol
Surface area34700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.850, 193.190, 191.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.07517, -0.046137, -0.996103), (-0.040167, -0.998258, 0.043206), (-0.996361, 0.036763, -0.076892)
Vector: 144.60181, 71.9865, 152.9706)

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Components

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


Mass: 45260.637 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Tissue: RETINA / Cell: ROD OUTER SEGMENTS / Cellular location: CYTOPLASM / Organ: EYE / Plasmid: PTRC / Production host: Escherichia coli (E. coli) / Strain (production host): ER2508 / References: UniProt: P08168
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.3 Å3/Da / Density % sol: 71 % / Description: BEAMLINES: APS, 19ID
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: used microseeding / PH range low: 8.8 / PH range high: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMTris-HCl1reservoir
2200 mMammonium acetate1reservoir
322-25 %isopropanol1reservoir
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1.00523
DetectorType: ADSC / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00523 Å / Relative weight: 1
ReflectionResolution: 2.8→60 Å / Num. obs: 242164 / % possible obs: 84.7 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 154.9 Å2 / Rsym value: 0.051 / Net I/σ(I): 11
Reflection shellResolution: 2.8→2.86 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 2 / Rsym value: 0.342 / % possible all: 42

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
PHASESphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.8→45 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 7316256.45 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1762 2.5 %RANDOM
Rwork0.233 ---
obs0.233 69807 91.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.45 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 59.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.4 Å20 Å20 Å2
2--6.98 Å20 Å2
3----2.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 2.8→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11675 0 0 25 11700
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.441.5
X-RAY DIFFRACTIONc_mcangle_it5.622
X-RAY DIFFRACTIONc_scbond_it5.452
X-RAY DIFFRACTIONc_scangle_it7.972.5
Refine LS restraints NCSNCS model details: CONSTR / Weight Biso : 2 / Weight position: 300
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.456 187 2.8 %
Rwork0.44 6520 -
obs--52.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CIS_PEPTIDE.PARAM
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 45 Å / σ(F): 0 / % reflection Rfree: 2.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 59.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Rfactor Rfree: 0.456 / % reflection Rfree: 2.8 % / Rfactor Rwork: 0.44

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