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- PDB-5z39: Crystal structure of C terminal region of G-protein interacting p... -

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Basic information

Entry
Database: PDB / ID: 5z39
TitleCrystal structure of C terminal region of G-protein interacting protein 1 (Gip1) from Dictyostelium discoideum form II
ComponentsG-protein interacting protein 1
KeywordsPROTEIN BINDING / alpha helix / lipid binding / G-protein binding / social amoebae / chemotaxis
Function / homology
Function and homology information


chemotaxis to cAMP / establishment of protein localization to plasma membrane / heterotrimeric G-protein binding / G-protein beta/gamma-subunit complex binding / GTPase binding / regulation of apoptotic process / cytosol
Similarity search - Function
Tumor necrosis factor alpha-induced protein 8-like / Tumor necrosis factor alpha-induced protein 8-like superfamily / Domain of unknown function (DUF758) / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / PH domain-containing protein
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsMiyagawa, T. / Koteishi, H. / Kamimura, Y. / Miyanaga, Y. / Takeshita, K. / Nakagawa, A. / Ueda, M.
Funding support Japan, 3items
OrganizationGrant numberCountry
JSPS17K15105 Japan
JSPS17K07396 Japan
AMED-CRESTJP17gm0910001 Japan
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis of Gip1 for cytosolic sequestration of G protein in wide-range chemotaxis
Authors: Miyagawa, T. / Koteishi, H. / Kamimura, Y. / Miyanaga, Y. / Takeshita, K. / Nakagawa, A. / Ueda, M.
History
DepositionJan 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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: G-protein interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7564
Polymers19,3181
Non-polymers1,4383
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-11 kcal/mol
Surface area9400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.468, 43.618, 101.681
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein G-protein interacting protein 1


Mass: 19318.480 Da / Num. of mol.: 1 / Fragment: ligand binding domain, UNP residues 146-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: DDB0216772 / Plasmid: SUMOstar / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q55BQ2
#2: Chemical ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL


Mass: 691.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM
#3: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 1.92 Å3/Da / Density % sol: 35.97 % / Mosaicity: 0.15 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 14-20% PEG 20000, 100 mM Bicine, / PH range: 8.0-9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1.7 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 2.74→43.62 Å / Num. obs: 4277 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 46.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.034 / Rrim(I) all: 0.127 / Net I/σ(I): 18.9 / Num. measured all: 57795
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.74-2.8713.90.6115540.9360.1690.634100
9.09-43.6210.40.0441500.9990.0130.04699

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z1N

5z1n


Resolution: 2.74→40.085 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2703 425 10.02 %
Rwork0.2213 3817 -
obs0.2265 4242 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.76 Å2 / Biso mean: 42.2823 Å2 / Biso min: 18.49 Å2
Refinement stepCycle: final / Resolution: 2.74→40.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1348 0 53 7 1408
Biso mean--50.59 34.02 -
Num. residues----166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021430
X-RAY DIFFRACTIONf_angle_d0.4541913
X-RAY DIFFRACTIONf_chiral_restr0.036218
X-RAY DIFFRACTIONf_plane_restr0.003234
X-RAY DIFFRACTIONf_dihedral_angle_d10.1631231
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.74-3.13640.29531370.248712331370
3.1364-3.9510.31321390.2412601399
3.951-40.08980.23711490.201113241473

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