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- PDB-1fqi: RGS9 RGS DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1fqi
TitleRGS9 RGS DOMAIN
ComponentsREGULATOR OF G-PROTEIN SIGNALING 9
KeywordsSIGNALING PROTEIN / RGS9 / Phototransduction / rod / RGS / GAP
Function / homology
Function and homology information


regulation of G protein-coupled receptor signaling pathway / negative regulation of signal transduction / visual perception / GTPase activator activity / photoreceptor disc membrane / intracellular signal transduction / neuron projection / G protein-coupled receptor signaling pathway / plasma membrane / cytoplasm
Similarity search - Function
: / : / : / Regulator of G-protein signalling, DHEX domain / Regulator of G-protein signalling DHEX domain / Regulator of G-protein Signalling 4; domain 1 - #10 / Regulator of G-protein Signalling 4; domain 1 / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) ...: / : / : / Regulator of G-protein signalling, DHEX domain / Regulator of G-protein signalling DHEX domain / Regulator of G-protein Signalling 4; domain 1 - #10 / Regulator of G-protein Signalling 4; domain 1 / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / GGL domain / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Regulator of G-protein signaling 9
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.94 Å
AuthorsSlep, K.C. / Kercher, M.A. / He, W. / Cowan, C.W. / Wensel, T.G. / Sigler, P.B.
CitationJournal: Nature / Year: 2001
Title: Structural determinants for regulation of phosphodiesterase by a G protein at 2.0 A.
Authors: Slep, K.C. / Kercher, M.A. / He, W. / Cowan, C.W. / Wensel, T.G. / Sigler, P.B.
History
DepositionSep 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: REGULATOR OF G-PROTEIN SIGNALING 9


Theoretical massNumber of molelcules
Total (without water)17,6541
Polymers17,6541
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.309, 71.836, 34.625
Angle α, β, γ (deg.)90.00, 96.13, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-63-

HOH

21A-65-

HOH

31A-77-

HOH

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Components

#1: Protein REGULATOR OF G-PROTEIN SIGNALING 9 / RGS9


Mass: 17653.652 Da / Num. of mol.: 1 / Fragment: RGS DOMAIN (RESIDUES 276-422)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: O46469
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.4 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15.5% PEG8000, 50mM Tris pH8.0, 5% Ethylene Glycol, 75mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
215.5 %PEG80001reservoir
350 mMTris1reservoir
45 %ethylene glycol1reservoir
575 mM1reservoirNaCl

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0283, 0.9795, 0.9793, 0.9351
Detector
TypeIDDetectorDate
APS-11CCDMay 1, 1999
2Apr 30, 1999
3Apr 30, 1999
4May 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.02831
20.97951
30.97931
40.93511
ReflectionResolution: 1.94→50 Å / Num. all: 23872 / Num. obs: 23300 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 23.5
Reflection shellResolution: 1.94→2.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.301 / Num. unique all: 911 / % possible all: 91.9
Reflection shell
*PLUS
% possible obs: 91.9 % / Mean I/σ(I) obs: 3.1

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.94→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1020520.69 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2120 9.3 %RANDOM; 9.3%
Rwork0.223 ---
obs0.223 22730 95.1 %-
all-174154 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.93 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso mean: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.91 Å20 Å2-2.44 Å2
2--2.36 Å20 Å2
3---1.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.94→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1151 0 0 130 1281
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d1.504
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.94→2.06 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 323 9.4 %
Rwork0.263 3096 -
obs--86.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 9.3 % / Rfactor obs: 0.221 / Rfactor Rfree: 0.248
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74
LS refinement shell
*PLUS
Rfactor Rfree: 0.27 / % reflection Rfree: 9.4 % / Rfactor Rwork: 0.263 / Rfactor obs: 0.256

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