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- PDB-1fgy: GRP1 PH DOMAIN WITH INS(1,3,4,5)P4 -

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Basic information

Entry
Database: PDB / ID: 1fgy
TitleGRP1 PH DOMAIN WITH INS(1,3,4,5)P4
ComponentsGRP1
KeywordsSIGNALING PROTEIN / PH DOMAIN
Function / homology
Function and homology information


Intra-Golgi traffic / Golgi vesicle transport / establishment of epithelial cell polarity / regulation of ARF protein signal transduction / phosphatidylinositol-3,4,5-trisphosphate binding / bicellular tight junction / ruffle / positive regulation of cell adhesion / guanyl-nucleotide exchange factor activity / adherens junction ...Intra-Golgi traffic / Golgi vesicle transport / establishment of epithelial cell polarity / regulation of ARF protein signal transduction / phosphatidylinositol-3,4,5-trisphosphate binding / bicellular tight junction / ruffle / positive regulation of cell adhesion / guanyl-nucleotide exchange factor activity / adherens junction / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. ...Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE / Cytohesin-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsLietzke, S.E. / Bose, S. / Cronin, T. / Klarlund, J. / Chawla, A. / Czech, M.P. / Lambright, D.G.
CitationJournal: Mol.Cell / Year: 2000
Title: Structural basis of 3-phosphoinositide recognition by pleckstrin homology domains.
Authors: Lietzke, S.E. / Bose, S. / Cronin, T. / Klarlund, J. / Chawla, A. / Czech, M.P. / Lambright, D.G.
History
DepositionJul 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: GRP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6192
Polymers15,1191
Non-polymers5001
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.3, 107.0, 36.9
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein GRP1 / ARF1 GUANINE NUCLEOTIDE EXCHANGE FACTOR AND INTEGRIN BINDING PROTEIN HOMOLOG


Mass: 15118.962 Da / Num. of mol.: 1 / Fragment: PLECKSTRIN HOMOLOGY DOMAIN (RESIDUES 261 - 387)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: O08967
#2: Chemical ChemComp-4IP / INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE


Mass: 500.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H16O18P4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.69 Å3/Da / Density % sol: 54.36 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 4.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlcomplex1drop
26-8 %PEG40001reservoir
350 mMsodium acetate1reservoir
4100 mM1reservoirLiSO4
510 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9915
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9915 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. all: 24163 / Num. obs: 24163 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.1
Reflection shellResolution: 1.54→1.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.327 / % possible all: 85.3
Reflection shell
*PLUS
% possible obs: 85.3 % / Mean I/σ(I) obs: 3.9

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Processing

Software
NameVersionClassification
SHARPphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.5→6 Å / σ(F): 2 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.247 1055 RANDOM
Rwork0.213 --
all-24129 -
obs-22749 -
Refinement stepCycle: LAST / Resolution: 1.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1058 0 28 136 1222
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.3

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