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- PDB-4igu: Crystal structure of the RGS domain of CG5036 -

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Basic information

Entry
Database: PDB / ID: 4igu
TitleCrystal structure of the RGS domain of CG5036
ComponentsCG5036
KeywordsSIGNALING PROTEIN / REGULATOR OF G-PROTEIN SIGNALING / GTPASE-ACTIVATING PROTEINS (GAP) / REGULATOR OF GZ-SELECTIVE PROTEIN SIGNALING 2
Function / homology
Function and homology information


G alpha (z) signalling events / G alpha (q) signalling events / G alpha (i) signalling events / GDP-dissociation inhibitor activity / G-protein alpha-subunit binding / GTPase activator activity / positive regulation of GTPase activity
Similarity search - Function
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 domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Double hit, isoform B
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGabdulkhakov, A. / Tishchenko, S.
CitationJournal: Mol.Cell / Year: 2014
Title: Double suppression of the G alpha protein activity by RGS proteins
Authors: Lin, C. / Koval, A. / Tishchenko, S. / Gabdulkhakov, A. / Tin, U. / Solis, G.P. / Katanaev, V.L.
History
DepositionDec 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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: CG5036
B: CG5036
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,38110
Polymers35,0962
Non-polymers2858
Water3,315184
1
A: CG5036
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6775
Polymers17,5481
Non-polymers1294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CG5036
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7045
Polymers17,5481
Non-polymers1564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-77 kcal/mol
Surface area15520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.393, 65.980, 141.701
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CG5036 / LD40005p


Mass: 17547.889 Da / Num. of mol.: 2 / Fragment: RGC domain, UNP residues 130-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG5036, Dmel_CG5036, EG:52C10.2 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15(pREP4) / References: UniProt: Q8T017
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.16 Å3/Da / Density % sol: 42.99 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% Jeffamine ED-2001, 0.1M HEPES , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54178 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Nov 14, 2012
RadiationMonochromator: Montel 200 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 45976 / Num. obs: 45971 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.95 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZV4

1zv4


Resolution: 1.9→27.046 Å / SU ML: 0.21 / σ(F): 1.3 / Phase error: 21.72 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 2344 5.11 %RANDOM
Rwork0.1836 ---
all0.187 45971 --
obs0.1861 45913 99.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→27.046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2284 0 11 184 2479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072374
X-RAY DIFFRACTIONf_angle_d0.9373204
X-RAY DIFFRACTIONf_dihedral_angle_d14.296939
X-RAY DIFFRACTIONf_chiral_restr0.06347
X-RAY DIFFRACTIONf_plane_restr0.005416
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.93880.35721260.2905247997
1.9388-1.9810.33821260.2626249498
1.981-2.0270.321720.2313258399
2.027-2.07770.26781480.2163246699
2.0777-2.13380.21651260.20332650100
2.1338-2.19660.24521000.19332570100
2.1966-2.26750.22731370.18932582100
2.2675-2.34850.20531400.18432587100
2.3485-2.44240.2621530.18072556100
2.4424-2.55350.22381330.17652602100
2.5535-2.6880.22531490.18182579100
2.688-2.85630.22681380.19152550100
2.8563-3.07650.25521400.1912599100
3.0765-3.38560.25191710.17922530100
3.3856-3.87430.20141260.162259499
3.8743-4.87650.15271340.13872565100
4.8765-27.0490.20361250.1572583100

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