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- PDB-1u2b: Triglycine variant of the Grp1 Pleckstrin Homology Domain unliganded -

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Basic information

Entry
Database: PDB / ID: 1u2b
TitleTriglycine variant of the Grp1 Pleckstrin Homology Domain unliganded
ComponentsCytohesin 3
KeywordsLIPID BINDING PROTEIN / PH domain / lipid binding / phosphoinositides
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 / cytoplasm / cytosol
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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCronin, T.C. / DiNitto, J.P. / Czech, M.P. / Lambright, D.G.
CitationJournal: Embo J. / Year: 2004
Title: Structural determinants of phosphoinositide selectivity in splice variants of Grp1 family PH domains
Authors: Cronin, T.C. / DiNitto, J.P. / Czech, M.P. / Lambright, D.G.
History
DepositionJul 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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_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_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

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Assembly

Deposited unit
A: Cytohesin 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4523
Polymers16,2591
Non-polymers1922
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.794, 107.514, 37.359
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Cytohesin 3 / ARF nucleotide-binding site opener 3 / ARNO3 protein / General receptor of phosphoinositides 1 / Grp1 / CLM-3


Mass: 16259.445 Da / Num. of mol.: 1 / Fragment: PH
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pscd3, Grp1 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O08967
#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.: 76 / 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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: PEG 4000, sodium acetate, 10% glycerol, lithium sulfate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 19, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 15937 / Num. obs: 15719 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.8→1.85 Å / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FGY

1fgy


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.746 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.128 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Hydrogens have been added in the riding positions. Several atoms for residues 280, 323, 334, 335, 336, 353, 355, 370 and 387 were modeled into this structure with zero occupancy because they ...Details: Hydrogens have been added in the riding positions. Several atoms for residues 280, 323, 334, 335, 336, 353, 355, 370 and 387 were modeled into this structure with zero occupancy because they are part of the PH domain and were not deleted or mutated.
RfactorNum. reflection% reflectionSelection details
Rfree0.24004 784 5 %RANDOM
Rwork0.21786 ---
all0.21897 15086 --
obs0.21897 14899 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.028 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20 Å2
2--0.82 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1057 0 10 76 1143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221032
X-RAY DIFFRACTIONr_bond_other_d0.0020.02918
X-RAY DIFFRACTIONr_angle_refined_deg1.1361.9561401
X-RAY DIFFRACTIONr_angle_other_deg0.72432139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9855122
X-RAY DIFFRACTIONr_chiral_restr0.070.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021124
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02216
X-RAY DIFFRACTIONr_nbd_refined0.190.2170
X-RAY DIFFRACTIONr_nbd_other0.2430.2976
X-RAY DIFFRACTIONr_nbtor_other0.0820.2619
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.255
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2670.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0960.24
X-RAY DIFFRACTIONr_mcbond_it0.7661.5621
X-RAY DIFFRACTIONr_mcangle_it1.42421001
X-RAY DIFFRACTIONr_scbond_it1.6183411
X-RAY DIFFRACTIONr_scangle_it2.664.5400
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.22 59
Rwork0.27 1052

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