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- PDB-2p0d: ArhGAP9 PH domain in complex with Ins(1,4,5)P3 -

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Basic information

Entry
Database: PDB / ID: 2p0d
TitleArhGAP9 PH domain in complex with Ins(1,4,5)P3
ComponentsRho GTPase-activating protein 9
KeywordsLIGAND BINDING PROTEIN / Protein-phosphoinositide complex / Pleckstrin homology domain
Function / homology
Function and homology information


regulation of small GTPase mediated signal transduction / phosphatidylinositol-3,4,5-trisphosphate binding / RHOA GTPase cycle / CDC42 GTPase cycle / regulation of GTPase activity / RAC1 GTPase cycle / GTPase activator activity / secretory granule lumen / Neutrophil degranulation / signal transduction ...regulation of small GTPase mediated signal transduction / phosphatidylinositol-3,4,5-trisphosphate binding / RHOA GTPase cycle / CDC42 GTPase cycle / regulation of GTPase activity / RAC1 GTPase cycle / GTPase activator activity / secretory granule lumen / Neutrophil degranulation / signal transduction / extracellular region / cytosol / cytoplasm
Similarity search - Function
Rho GTPase-activating protein 9, SH3 domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / WW domain superfamily / WW/rsp5/WWP domain profile. / WW domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) ...Rho GTPase-activating protein 9, SH3 domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / WW domain superfamily / WW/rsp5/WWP domain profile. / WW domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Rho GTPase-activating protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.811 Å
AuthorsCeccarelli, D.F.J. / Blasutig, I. / Goudreault, M. / Ruston, J. / Pawson, T. / Sicheri, F.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Non-canonical Interaction of Phosphoinositides with Pleckstrin Homology Domains of Tiam1 and ArhGAP9.
Authors: Ceccarelli, D.F. / Blasutig, I.M. / Goudreault, M. / Li, Z. / Ruston, J. / Pawson, T. / Sicheri, F.
History
DepositionFeb 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho GTPase-activating protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8452
Polymers14,4251
Non-polymers4201
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.510, 95.110, 29.700
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 Rho GTPase-activating protein 9


Mass: 14425.402 Da / Num. of mol.: 1 / Fragment: Pleckstrin homology domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGAP9 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon plus / References: UniProt: Q9BRR9
#2: Chemical ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Inositol trisphosphate


Mass: 420.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15O15P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.03 Å3/Da / Density % sol: 39.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 26% PEG4000, 100mM HEPES, 10% glycerol, 5mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9202 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 29, 2004 / Details: bent-flat Si-mirror (Rh coated)
RadiationMonochromator: Si (111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 11480 / % possible obs: 99.2 % / Redundancy: 12 % / Rmerge(I) obs: 0.048 / Χ2: 1.096 / Net I/σ(I): 17
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.361 / Num. unique all: 1066 / Χ2: 1.072 / % possible all: 93.6

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation1.96 Å31.27 Å
Translation1.96 Å31.27 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.811→47.57 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.768 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 534 4.8 %RANDOM
Rwork0.199 ---
obs0.2 11190 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å20 Å2
2---0.39 Å20 Å2
3---1.22 Å2
Refinement stepCycle: LAST / Resolution: 1.811→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms861 0 24 72 957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021906
X-RAY DIFFRACTIONr_angle_refined_deg1.9821.9581235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.375107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.76921.1942
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56215146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7221511
X-RAY DIFFRACTIONr_chiral_restr0.1530.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02670
X-RAY DIFFRACTIONr_nbd_refined0.2060.2355
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2600
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.262
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.29
X-RAY DIFFRACTIONr_mcbond_it1.8041.5552
X-RAY DIFFRACTIONr_mcangle_it1.8922850
X-RAY DIFFRACTIONr_scbond_it2.8733408
X-RAY DIFFRACTIONr_scangle_it4.4874.5384
LS refinement shellResolution: 1.811→1.858 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 33 -
Rwork0.28 714 -
obs-747 90.44 %

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