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- PDB-2oj4: Crystal structure of RGS3 RGS domain -

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Basic information

Entry
Database: PDB / ID: 2oj4
TitleCrystal structure of RGS3 RGS domain
ComponentsRegulator of G-protein signaling 3
KeywordsSIGNALING PROTEIN INHIBITOR / PROTEIN / RGS DOMAIN
Function / homology
Function and homology information


regulation of G protein-coupled receptor signaling pathway / negative regulation of signal transduction / GTPase activator activity / G alpha (i) signalling events / G alpha (q) signalling events / G protein-coupled receptor signaling pathway / GTPase activity / nucleus / plasma membrane / cytosol
Similarity search - Function
Regulator of G-protein signalling 3, RGS 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 3, RGS 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 / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Regulator of G-protein signaling 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBoura, E. / Obsil, T.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: 14-3-3 protein interacts with and affects the structure of RGS domain of regulator of G protein signaling 3 (RGS3).
Authors: Rezabkova, L. / Boura, E. / Herman, P. / Vecer, J. / Bourova, L. / Sulc, M. / Svoboda, P. / Obsilova, V. / Obsil, T.
History
DepositionJan 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 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
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: Regulator of G-protein signaling 3


Theoretical massNumber of molelcules
Total (without water)14,8951
Polymers14,8951
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.236, 60.849, 57.406
Angle α, β, γ (deg.)90.00, 135.44, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-132-

HOH

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Components

#1: Protein Regulator of G-protein signaling 3 / RGS3 / RGP3


Mass: 14895.071 Da / Num. of mol.: 1 / Fragment: RGS domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RGS3 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P49796
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 3.18 Å3/Da / Density % sol: 61.28 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 28% PEG 4000, 0.15M magnesium chloride, 0.1M glycine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 14, 2006 / Details: mirrors
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→28 Å / Num. all: 8099 / Num. obs: 8095 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 37.3 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 5.3 / Num. unique all: 1177 / % possible all: 97.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2refinement
MAR345345DTBdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FQI

1fqi


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.904 / SU B: 5.673 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.266 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 373 4.6 %RANDOM
Rwork0.193 ---
all0.221 8085 --
obs0.221 8085 96.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20.07 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1047 0 0 62 1109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221067
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.891.9621429
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9165126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.95724.3453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.77815209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.944156
X-RAY DIFFRACTIONr_chiral_restr0.1310.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02789
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.2479
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.2736
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.254
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.226
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3231.5664
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.16521008
X-RAY DIFFRACTIONr_scbond_it3.3633483
X-RAY DIFFRACTIONr_scangle_it4.9994.5421
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 33 -
Rwork0.203 560 -
obs--97.53 %

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