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- PDB-3c7l: Molecular architecture of Galphao and the structural basis for RG... -

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Basic information

Entry
Database: PDB / ID: 3c7l
TitleMolecular architecture of Galphao and the structural basis for RGS16-mediated deactivation
ComponentsRegulator of G-protein signaling 16
KeywordsSIGNALING PROTEIN / RGS / RGS16 / GAP / GTPase Activating Protein / Heterotrimeric G-protein / Lipoprotein / Palmitate / Phosphoprotein / Signal transduction inhibitor
Function / homology
Function and homology information


G alpha (z) signalling events / G alpha (q) signalling events / G alpha (i) signalling events / negative regulation of signal transduction / GTPase activator activity / positive regulation of GTPase activity / G protein-coupled receptor signaling pathway / membrane / cytoplasm
Similarity search - Function
Regulator of G-protein Signalling 4; domain 1 - #10 / Regulator of G-protein Signalling 4; domain 1 / RGS, subdomain 1/3 / 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 ...Regulator of G-protein Signalling 4; domain 1 - #10 / Regulator of G-protein Signalling 4; domain 1 / RGS, subdomain 1/3 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Regulator of G-protein signaling 16
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsSlep, K.C. / Kercher, M.A. / Wieland, T. / Chen, C. / Simon, M.I. / Sigler, P.B.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Molecular architecture of G{alpha}o and the structural basis for RGS16-mediated deactivation.
Authors: Slep, K.C. / Kercher, M.A. / Wieland, T. / Chen, C.K. / Simon, M.I. / Sigler, P.B.
History
DepositionFeb 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulator of G-protein signaling 16
B: Regulator of G-protein signaling 16


Theoretical massNumber of molelcules
Total (without water)31,6712
Polymers31,6712
Non-polymers00
Water3,225179
1
A: Regulator of G-protein signaling 16


Theoretical massNumber of molelcules
Total (without water)15,8361
Polymers15,8361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Regulator of G-protein signaling 16


Theoretical massNumber of molelcules
Total (without water)15,8361
Polymers15,8361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.379, 71.700, 72.306
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Regulator of G-protein signaling 16 / RGS16 / Retinally abundant regulator of G-protein signaling / RGS-R / A28-RGS14P


Mass: 15835.663 Da / Num. of mol.: 2 / Fragment: Residues 53-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rgs16, Rgsr / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P97428
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 1.94 Å3/Da / Density % sol: 36.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 34% PEG 400 150 mM ammonium citrate 100 mM cacodylate pH 6.5 0.5 mM KCl6Ir(IV), VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Oct 1, 1999 / Details: X25 optics
RadiationMonochromator: X25 monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. all: 21560 / Num. obs: 20395 / % possible obs: 94.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Biso Wilson estimate: 14.3 Å2 / Rsym value: 0.043 / Net I/σ(I): 21.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.004data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AGR

1agr


Resolution: 1.89→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1896 9.3 %Random
Rwork0.222 ---
obs-19238 94.6 %-
Solvent computationBsol: 45.994 Å2
Displacement parametersBiso mean: 14.49 Å2
Baniso -1Baniso -2Baniso -3
1-1.183 Å20 Å20 Å2
2---2.327 Å20 Å2
3---1.144 Å2
Refinement stepCycle: LAST / Resolution: 1.89→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 0 179 2235
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.021
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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