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- PDB-2f5y: Crystal Structure of the PDZ Domain from Human RGS-3 -

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Basic information

Entry
Database: PDB / ID: 2f5y
TitleCrystal Structure of the PDZ Domain from Human RGS-3
Componentsregulator of G-protein signalling 3 isoform 1
KeywordsSIGNALING PROTEIN / PDZ Domain / RGS-3 / Human / Structural Genomics / Structural Genomics Consortium / SGC
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, 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) ...Regulator of G-protein signalling 3, RGS domain / RGS, subdomain 1/3 / 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. / PDZ domain / Pdz3 Domain / 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 / Roll / Mainly Beta
Similarity search - Domain/homology
Regulator of G-protein signaling 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsUgochukwu, E. / Berridge, G. / Johansson, C. / Smee, C. / Savitsky, P. / Burgess, N. / Colebrook, S. / Yang, X. / Elkins, J. / Doyle, D. ...Ugochukwu, E. / Berridge, G. / Johansson, C. / Smee, C. / Savitsky, P. / Burgess, N. / Colebrook, S. / Yang, X. / Elkins, J. / Doyle, D. / Turnbull, A. / Papagrigoriou, E. / Debreczeni, J. / Bunkoczi, G. / Gorrec, F. / von Delft, F. / Arrowsmith, C. / Sundstrom, M. / Weigelt, J. / Edwards, A. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of the PDZ Domain from Human RGS-3
Authors: Ugochukwu, E. / Berridge, G. / Johansson, C. / Smee, C. / Savitsky, P. / Burgess, N. / Colebrook, S. / Yang, X. / Elkins, J. / Doyle, D. / Turnbull, A. / Papagrigoriou, E. / Debreczeni, J. / ...Authors: Ugochukwu, E. / Berridge, G. / Johansson, C. / Smee, C. / Savitsky, P. / Burgess, N. / Colebrook, S. / Yang, X. / Elkins, J. / Doyle, D. / Turnbull, A. / Papagrigoriou, E. / Debreczeni, J. / Bunkoczi, G. / Gorrec, F. / von Delft, F. / Arrowsmith, C. / Sundstrom, M. / Weigelt, J. / Edwards, A.
History
DepositionNov 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: regulator of G-protein signalling 3 isoform 1
B: regulator of G-protein signalling 3 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6724
Polymers20,4802
Non-polymers1922
Water75742
1
A: regulator of G-protein signalling 3 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4323
Polymers10,2401
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: regulator of G-protein signalling 3 isoform 1


Theoretical massNumber of molelcules
Total (without water)10,2401
Polymers10,2401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.110, 44.140, 49.857
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 4 / Auth seq-ID: 14 - 95 / Label seq-ID: 2 - 83

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein regulator of G-protein signalling 3 isoform 1


Mass: 10239.818 Da / Num. of mol.: 2 / Fragment: PDZ Domain (residues 15-103)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: BL21 (DE3) / Gene: RGS3 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: P49796
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6M ammonium sulphate, 0.1M MES, 10% dioxane, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9788 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 22, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.39→49.86 Å / Num. obs: 8381 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.49 Å / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I92.pdb, 1QAU.pdb

1i92

1qau


Resolution: 2.39→49.88 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.899 / SU B: 15.045 / SU ML: 0.177 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.369 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26429 386 4.6 %RANDOM
Rwork0.21481 ---
all0.21698 7967 --
obs0.21698 7967 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.859 Å2
Baniso -1Baniso -2Baniso -3
1--2.18 Å20 Å20 Å2
2--4.63 Å20 Å2
3----2.45 Å2
Refinement stepCycle: LAST / Resolution: 2.39→49.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1267 0 10 42 1319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221310
X-RAY DIFFRACTIONr_bond_other_d0.0030.02921
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.9681779
X-RAY DIFFRACTIONr_angle_other_deg1.5243.0042223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.5735164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2921.96456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.59815223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6631516
X-RAY DIFFRACTIONr_chiral_restr0.2030.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021437
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02268
X-RAY DIFFRACTIONr_nbd_refined0.20.2223
X-RAY DIFFRACTIONr_nbd_other0.2010.21020
X-RAY DIFFRACTIONr_nbtor_refined0.1660.2612
X-RAY DIFFRACTIONr_nbtor_other0.0880.2763
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.254
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1370.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0930.24
X-RAY DIFFRACTIONr_mcbond_it3.1223856
X-RAY DIFFRACTIONr_mcbond_other1.0583331
X-RAY DIFFRACTIONr_mcangle_it4.15251327
X-RAY DIFFRACTIONr_scbond_it6.8077523
X-RAY DIFFRACTIONr_scangle_it8.9911451
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1042 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.550.5
medium thermal0.832
LS refinement shellResolution: 2.394→2.456 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 31 -
Rwork0.244 559 -
obs--97.2 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.34080.83941.0525.41782.00346.54060.16-0.1435-0.00450.1205-0.2332-0.02150.10480.0070.0732-0.2384-0.0032-0.0152-0.17880.017-0.198311.5012-4.6324-21.7192
24.5605-1.20580.33626.65321.58616.0421-0.02240.3398-0.0193-0.3723-0.12320.6764-0.0952-0.28810.1456-0.1728-0.0071-0.0487-0.1803-0.011-0.128911.1807-16.5929-43.8321
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA14 - 952 - 83
2X-RAY DIFFRACTION2BB14 - 952 - 83

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