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- PDB-3qc9: Crystal structure of cross-linked bovine GRK1 T8C/N480C double mu... -

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Basic information

Entry
Database: PDB / ID: 3qc9
TitleCrystal structure of cross-linked bovine GRK1 T8C/N480C double mutant complexed with ADP and Mg
ComponentsRhodopsin kinase
KeywordsTRANSFERASE / enkaryotic protein kinase fold / protein serine/threonine kinase
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'-DIPHOSPHATE / Rhodopsin kinase GRK1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHuang, C.-C. / Tesmer, J.J.G.
CitationJournal: Biochemistry / Year: 2011
Title: Activation of G Protein-Coupled Receptor Kinase 1 Involves Interactions between Its N-Terminal Region and Its Kinase Domain.
Authors: Huang, C.C. / Orban, T. / Jastrzebska, B. / Palczewski, K. / Tesmer, J.J.
History
DepositionJan 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhodopsin kinase
B: Rhodopsin kinase
C: Rhodopsin kinase
D: Rhodopsin kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,77118
Polymers245,6844
Non-polymers2,08714
Water2,036113
1
A: Rhodopsin kinase
D: Rhodopsin kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,8869
Polymers122,8422
Non-polymers1,0447
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-54 kcal/mol
Surface area45290 Å2
MethodPISA
2
B: Rhodopsin kinase
C: Rhodopsin kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,8869
Polymers122,8422
Non-polymers1,0447
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-54 kcal/mol
Surface area45060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.696, 89.965, 122.638
Angle α, β, γ (deg.)88.07, 90.26, 68.78
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and resid 31:533
211chain B and resid 31:533
311chain C and resid 31:533
411chain D and resid 31:533
DetailsACCORDING TO THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN. HOWEVER, THE MONOMERIC STATE IS FUNCTIONAL IN SOLUTION

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Components

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


Mass: 61421.012 Da / Num. of mol.: 4 / Fragment: UNP residues 1-535 / Mutation: T8C, N480C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: GRK1, RHOK / Cell line (production host): High 5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P28327, rhodopsin kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.46 Å3/Da / Density % sol: 49.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 14-19% PEG 3350, 0.1 M Bis-Tris pH 5.5, 0.15 M MgCl2, and 0.02% n-dodecyl- D-maltoside, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 2, 2009
RadiationMonochromator: diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 64625 / Num. obs: 61717 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 15
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.451 / % possible all: 95.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3C4Z
Resolution: 2.7→29.599 Å / SU ML: 0.34 / σ(F): 1 / Phase error: 26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2286 2897 5.06 %
Rwork0.1924 --
obs0.1943 57246 89.18 %
all-64191 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.025 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-11.1488 Å26.3631 Å2-1.1873 Å2
2--8.4486 Å23.6521 Å2
3----19.5974 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15565 0 128 113 15806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816094
X-RAY DIFFRACTIONf_angle_d1.19821727
X-RAY DIFFRACTIONf_dihedral_angle_d17.1046055
X-RAY DIFFRACTIONf_chiral_restr0.0752269
X-RAY DIFFRACTIONf_plane_restr0.0042825
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3873X-RAY DIFFRACTIONPOSITIONAL
12B3873X-RAY DIFFRACTIONPOSITIONAL0.043
13C3880X-RAY DIFFRACTIONPOSITIONAL0.036
14D3905X-RAY DIFFRACTIONPOSITIONAL0.044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.79650.3882470.30854726X-RAY DIFFRACTION77
2.7965-2.90830.33432780.28034926X-RAY DIFFRACTION81
2.9083-3.04060.34572730.25595102X-RAY DIFFRACTION84
3.0406-3.20070.2672600.2395288X-RAY DIFFRACTION87
3.2007-3.4010.28363070.21365395X-RAY DIFFRACTION88
3.401-3.66310.25123080.20065533X-RAY DIFFRACTION91
3.6631-4.03090.24553040.18815632X-RAY DIFFRACTION93
4.0309-4.61230.17853030.15375826X-RAY DIFFRACTION95
4.6123-5.80380.18433090.15825963X-RAY DIFFRACTION98
5.8038-29.60070.17713080.17545958X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.1174-0.02090.17930.0677-0.10871.10050.06260.0452-0.0234-0.0257-0.00050.03730.1710.1813-0.06240.22380.041-0.0270.2234-0.02610.2107-30.2211-10.753649.6961
20.2133-0.0530.3562-0.10.05891.26730.00620.02360.0021-0.00870.03370.00660.0770.0776-0.03270.2546-0.0380.00740.2139-0.00040.2447-42.1369-53.044844.4895
30.04690.01920.11160.0697-0.16250.46760.0317-0.0124-0.00190.02460.0093-0.0252-0.0824-0.033-0.03590.22140.03030.00840.19750.01930.2321-53.9075-51.7895-13.2996
40.2234-0.1104-0.1365-0.00610.25010.8380.02450.02870.0163-0.00780.0029-0.0219-0.15820.072300.2003-0.02030.0080.16870.01350.2035-41.6764-9.504-15.4474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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