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- PDB-1suj: X-ray crystal structure of ambystoma tigrinum cone arrestin -

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Basic information

Entry
Database: PDB / ID: 1suj
TitleX-ray crystal structure of ambystoma tigrinum cone arrestin
Componentscone arrestin
KeywordsSIGNALING PROTEIN / sensory transduction
Function / homology
Function and homology information


visual perception / signal transduction
Similarity search - Function
Arrestin-C / 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-C / 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 speciesAmbystoma tigrinum (tiger salamander)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsSutton, R.B. / Navarro, J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal structure of cone arrestin at 2.3A: evolution of receptor specificity.
Authors: Sutton, R.B. / Vishnivetskiy, S.A. / Robert, J. / Hanson, S.M. / Raman, D. / Knox, B.E. / Kono, M. / Navarro, J. / Gurevich, V.V.
History
DepositionMar 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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: cone arrestin


Theoretical massNumber of molelcules
Total (without water)43,9591
Polymers43,9591
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.762, 75.049, 79.059
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein cone arrestin


Mass: 43959.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ambystoma tigrinum (tiger salamander) / Gene: ARR2 / Plasmid: pTrcHisB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9PTE7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG 5000, MME, 0.1 M bis-TRIS, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 13, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.36→50 Å / Num. obs: 17638 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 20
Reflection shellResolution: 2.36→2.47 Å / Mean I/σ(I) obs: 4.5 / % possible all: 82.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1CF1

1cf1


Resolution: 2.38→27.22 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1352813.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.297 1633 9.4 %RANDOM
Rwork0.246 ---
all0.25 ---
obs0.246 17425 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.825 Å2 / ksol: 0.315777 e/Å3
Displacement parametersBiso mean: 39.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.08 Å20 Å20 Å2
2---3.53 Å20 Å2
3---6.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.38→27.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2846 0 0 99 2945
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it1.851.5
X-RAY DIFFRACTIONc_mcangle_it3.272
X-RAY DIFFRACTIONc_scbond_it2.262
X-RAY DIFFRACTIONc_scangle_it3.382.5
LS refinement shellResolution: 2.38→2.53 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.362 307 10.7 %
Rwork0.302 2551 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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