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- PDB-1fhw: Structure of the pleckstrin homology domain from GRP1 in complex ... -

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Basic information

Entry
Database: PDB / ID: 1fhw
TitleStructure of the pleckstrin homology domain from GRP1 in complex with inositol(1,3,4,5,6)pentakisphosphate
ComponentsGUANINE NUCLEOTIDE EXCHANGE FACTOR AND INTEGRIN BINDING PROTEIN HOMOLOG GRP1
KeywordsSIGNALING PROTEIN / PLECKSTRIN / 3-PHOSPHOINOSITIDES / INOSITOL TETRAKISPHOSPHATE SIGNAL TRANSDUCTION PROTEIN / GUANINE NUCLEOTIDE EXCHANGE FACTOR
Function / homology
Function and homology information


Intra-Golgi traffic / regulation of ARF protein signal transduction / Golgi vesicle transport / establishment of epithelial cell polarity / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of cell adhesion / bicellular tight junction / ruffle / guanyl-nucleotide exchange factor activity / adherens junction ...Intra-Golgi traffic / regulation of ARF protein signal transduction / Golgi vesicle transport / establishment of epithelial cell polarity / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of cell adhesion / bicellular tight junction / ruffle / 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-(1,3,4,5,6)-PENTAKISPHOSPHATE / : / Cytohesin-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsFerguson, K.M. / Kavran, J.M. / Sankaran, V.G. / Fournier, E. / Isakoff, S.J. / Skolnik, E.Y. / Lemmon, M.A.
CitationJournal: Mol.Cell / Year: 2000
Title: Structural basis for discrimination of 3-phosphoinositides by pleckstrin homology domains
Authors: Ferguson, K.M. / Kavran, J.M. / Sankaran, V.G. / Fournier, E. / Isakoff, S.J. / Skolnik, E.Y. / Lemmon, M.A.
History
DepositionAug 2, 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: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GUANINE NUCLEOTIDE EXCHANGE FACTOR AND INTEGRIN BINDING PROTEIN HOMOLOG GRP1
B: GUANINE NUCLEOTIDE EXCHANGE FACTOR AND INTEGRIN BINDING PROTEIN HOMOLOG GRP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6955
Polymers30,4392
Non-polymers1,2563
Water2,954164
1
A: GUANINE NUCLEOTIDE EXCHANGE FACTOR AND INTEGRIN BINDING PROTEIN HOMOLOG GRP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7992
Polymers15,2191
Non-polymers5801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GUANINE NUCLEOTIDE EXCHANGE FACTOR AND INTEGRIN BINDING PROTEIN HOMOLOG GRP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8963
Polymers15,2191
Non-polymers6762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-60 kcal/mol
Surface area12660 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)37.970, 72.220, 46.900
Angle α, β, γ (deg.)90.00, 93.21, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer constructed from chain A or chain B

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Components

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


Mass: 15219.406 Da / Num. of mol.: 2 / Fragment: PLECKSTRIN HOMOLOGY DOMAIN
Source method: isolated from a genetically manipulated source
Details: COMPLEX WITH INOSITOL (1,3,4,5,6)-PENTAKISPHOSPHATE
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / References: GenBank: 2183209, UniProt: O08967*PLUS
#2: Chemical ChemComp-I5P / INOSITOL-(1,3,4,5,6)-PENTAKISPHOSPHATE


Mass: 580.055 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H17O21P5
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.11 Å3/Da / Density % sol: 29.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 8000, SODIUM ACETATE, AMMONIUM SULFATE, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12-10 %PEG80001reservoir
250 mMsodium acetate1reservoir
3200 mMammonium sulfate1reservoir
415 mg/mlprotein1drop
510 mMMES1drop
6100 mM1dropNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Feb 10, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 53932 / Num. obs: 18374 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 20
Reflection shellResolution: 1.9→1.96 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 10.7 / Rsym value: 0.08 / % possible all: 80.5
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 50 Å / Observed criterion σ(I): 0 / Num. measured all: 53932
Reflection shell
*PLUS
% possible obs: 80.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS0.9refinement
RefinementMethod to determine structure: MIR / Resolution: 1.9→46.83 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1114520.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1795 9.8 %RANDOM
Rwork0.229 ---
all0.229 18358 --
obs0.229 18358 91.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.4 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso mean: 27.3 Å2
Baniso -1Baniso -2Baniso -3
1-9.34 Å20 Å2-8.01 Å2
2---5.66 Å20 Å2
3----3.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 69 164 2245
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it2.411.5
X-RAY DIFFRACTIONc_mcangle_it2.882
X-RAY DIFFRACTIONc_scbond_it2.652
X-RAY DIFFRACTIONc_scangle_it3.772.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 225 10.2 %
Rwork0.229 1972 -
obs--66.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5PARAM.IP5TOP.IP5
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 500 Å / σ(F): 0 / % reflection Rfree: 9.8 % / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.284 / % reflection Rfree: 10.2 % / Rfactor Rwork: 0.229

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