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- PDB-3t8o: Rhodopsin kinase (GRK1) L166K mutant at 2.5A resolution -

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Basic information

Entry
Database: PDB / ID: 3t8o
TitleRhodopsin kinase (GRK1) L166K mutant at 2.5A resolution
ComponentsRhodopsin kinase
KeywordsTRANSFERASE / Kinase domain / RGS Homology (RH) domain / G-protein Receptor Kinase (GPCR)
Function / homology
Function and homology information


rhodopsin kinase / rhodopsin kinase activity / regulation of rhodopsin mediated signaling pathway / Inactivation, recovery and regulation of the phototransduction cascade / regulation of signal transduction / visual perception / photoreceptor disc membrane / protein kinase activity / protein autophosphorylation / protein phosphorylation ...rhodopsin kinase / rhodopsin kinase activity / regulation of rhodopsin mediated signaling pathway / Inactivation, recovery and regulation of the phototransduction cascade / regulation of signal transduction / visual perception / photoreceptor disc membrane / protein kinase activity / protein autophosphorylation / protein phosphorylation / signal transduction / ATP binding / cytoplasm
Similarity search - Function
Rhodopsin kinase GRK1 / Rhodopsin kinase, catalytic domain / GPCR kinase / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain ...Rhodopsin kinase GRK1 / Rhodopsin kinase, catalytic domain / GPCR kinase / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Phosphorylase Kinase; domain 1 / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Rhodopsin kinase GRK1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTesmer, J.J.G. / Singh, P. / Nance, M.R.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of a monomeric variant of rhodopsin kinase at 2.5 A resolution.
Authors: Tesmer, J.J. / Nance, M.R. / Singh, P. / Lee, H.
History
DepositionAug 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rhodopsin kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1055
Polymers61,4461
Non-polymers6594
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.541, 149.808, 190.879
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Rhodopsin kinase / / RK / G protein-coupled receptor kinase 1


Mass: 61445.957 Da / Num. of mol.: 1 / Fragment: UNP residues 1-535 / Mutation: L166K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: GRK1, RHOK / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi-5 / References: UniProt: P28327, rhodopsin kinase

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Non-polymers , 5 types, 56 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: 12% PEG 6000, 100 mM Na-citrate pH 4.3 and 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9999 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 27804 / % possible obs: 99.5 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.086 / Χ2: 1.216 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.598.10.79227321.036199
2.59-2.698.20.59827241.022199.1
2.69-2.828.30.45727281.005199.3
2.82-2.968.40.31727501.027199.5
2.96-3.158.40.20727441.062199.6
3.15-3.398.30.14127651.161199.8
3.39-3.738.30.09627861.357199.6
3.73-4.278.20.0628021.419199.5
4.27-5.388.10.04628201.612199.8
5.38-307.60.03629531.458199.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.6 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.2348 / WRfactor Rwork: 0.1954 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8109 / SU B: 20.213 / SU ML: 0.198 / SU R Cruickshank DPI: 0.3359 / SU Rfree: 0.2458 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2449 1403 5 %RANDOM
Rwork0.2068 ---
obs0.2088 27797 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 62.44 Å2 / Biso mean: 55.635 Å2 / Biso min: 4.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3960 0 39 52 4051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224123
X-RAY DIFFRACTIONr_bond_other_d0.0010.022918
X-RAY DIFFRACTIONr_angle_refined_deg1.541.9765568
X-RAY DIFFRACTIONr_angle_other_deg0.98837048
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0665496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64223.463205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.14815715
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.991534
X-RAY DIFFRACTIONr_chiral_restr0.0830.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214581
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02897
X-RAY DIFFRACTIONr_mcbond_it0.5621.52463
X-RAY DIFFRACTIONr_mcbond_other0.11.51004
X-RAY DIFFRACTIONr_mcangle_it1.0923936
X-RAY DIFFRACTIONr_scbond_it1.71931660
X-RAY DIFFRACTIONr_scangle_it2.8474.51631
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 85 -
Rwork0.334 1759 -
all-1844 -
obs--91.24 %
Refinement TLS params.Method: refined / Origin x: 1.4797 Å / Origin y: 23.7019 Å / Origin z: 28.8474 Å
111213212223313233
T0.156 Å20.0132 Å2-0.0487 Å2-0.1716 Å2-0.0122 Å2--0.0858 Å2
L1.9811 °20.2139 °2-0.5445 °2-2.315 °2-0.0405 °2--1.6553 °2
S0.0544 Å °0.1266 Å °0.3203 Å °-0.2466 Å °-0.0142 Å °0.2189 Å °-0.0251 Å °0.104 Å °-0.0403 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 532
2X-RAY DIFFRACTION1A544
3X-RAY DIFFRACTION1A545 - 599

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