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- PDB-3fbk: Crystal structure of the C2 domain of the human regulator of G-pr... -

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Basic information

Entry
Database: PDB / ID: 3fbk
TitleCrystal structure of the C2 domain of the human regulator of G-protein signaling 3 isoform 6 (RGP3), Northeast Structural Genomics Consortium Target HR5550A
ComponentsRegulator of G-protein signaling 3
KeywordsSIGNALING PROTEIN / all beta-sheet fold / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Alternative splicing / Cell membrane / Cytoplasm / Membrane / Nucleus / Phosphoprotein / Signal transduction inhibitor
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 / RGS, subdomain 1/3 / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / C2 domain / Protein kinase C conserved region 2 (CalB) ...Regulator of G-protein signalling 3, RGS domain / RGS, subdomain 1/3 / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Regulator of G-protein signaling 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsForouhar, F. / Lew, S. / Seetharaman, J. / Mao, L. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Shastry, R. / Everett, J.K. / Nair, R. ...Forouhar, F. / Lew, S. / Seetharaman, J. / Mao, L. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the C2 domain of the human regulator of G-protein signaling 3 isoform 6 (RGP3), Northeast Structural Genomics Consortium Target HR5550A
Authors: Forouhar, F. / Lew, S. / Seetharaman, J. / Mao, L. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionNov 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulator of G-protein signaling 3
B: Regulator of G-protein signaling 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6104
Polymers35,4182
Non-polymers1922
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-32 kcal/mol
Surface area13680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.661, 77.171, 44.681
Angle α, β, γ (deg.)90.00, 115.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 17709.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RGS3 / Plasmid: pET14-15C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P49796
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 37.54 %
Crystal growTemperature: 291 K / Method: microbatch under oil / pH: 7
Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 100 mM Bis-Tris Propane (pH 7), 40% PEG 1000, and 100 mM (NH4)2 SO4. , microbatch under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97905 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 13, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97905 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 36846 / Num. obs: 35631 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 6.6 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.058 / Net I/σ(I): 16.16
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 4.91 / Num. unique all: 3712 / Rsym value: 0.15 / % possible all: 94.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
RESOLVEmodel building
XTALVIEW& CNS 1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→19.58 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 650860.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1628 5 %RANDOM
Rwork0.198 ---
all0.199 36479 --
obs0.198 32540 89.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.9417 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 21.3 Å2
Baniso -1Baniso -2Baniso -3
1--4.68 Å20 Å2-2.54 Å2
2--7.64 Å20 Å2
3----2.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 2→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2222 0 10 170 2402
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
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: 2→2.07 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.257 158 5.7 %
Rwork0.203 2601 -
obs-2601 75.4 %

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