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- PDB-2p0f: ArhGAP9 PH domain in complex with Ins(1,3,5)P3 -

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Basic information

Entry
Database: PDB / ID: 2p0f
TitleArhGAP9 PH domain in complex with Ins(1,3,5)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 / CDC42 GTPase cycle / RHOA GTPase cycle / RAC1 GTPase cycle / GTPase activator activity / secretory granule lumen / Neutrophil degranulation / signal transduction / extracellular region ...regulation of small GTPase mediated signal transduction / phosphatidylinositol-3,4,5-trisphosphate binding / CDC42 GTPase cycle / RHOA GTPase cycle / RAC1 GTPase cycle / GTPase activator activity / secretory granule lumen / Neutrophil degranulation / signal transduction / extracellular region / cytoplasm / cytosol
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. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / WW domain ...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. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / WW domain / 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
PHOSPHATE ION / Rho GTPase-activating protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 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
Revision 1.4Aug 30, 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: Rho GTPase-activating protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5202
Polymers14,4251
Non-polymers951
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.751, 36.601, 113.708
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.12 Å3/Da / Density % sol: 42.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG4000, 100mM HEPES, 5% 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-C / Wavelength: 0.9002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 18, 2004 / Details: bent-flat Si-mirror (Rh coated)
RadiationMonochromator: Si (111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 9223 / % possible obs: 93.1 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.4
Reflection shell
Resolution (Å)Rmerge(I) obs% possible all
1.9-1.970.29191.3
1.97-2.050.22489.2
2.05-2.140.15792
2.14-2.250.12491
2.25-2.390.10793
2.39-2.580.09292.4
2.58-2.840.0792.6
2.84-3.250.04996.8
3.25-4.090.03599.1
4.09-250.02993.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1DRO

1dro


Resolution: 1.91→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.169 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23014 438 4.8 %RANDOM
Rwork0.2093 ---
obs0.21028 8744 92.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.745 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2--1.46 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.91→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms927 0 5 48 980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021956
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.681.9471299
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9715118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.55121.2241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83315154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2421511
X-RAY DIFFRACTIONr_chiral_restr0.1190.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02727
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.2395
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.2647
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.239
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2840.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8441.5613
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0232948
X-RAY DIFFRACTIONr_scbond_it3.2483399
X-RAY DIFFRACTIONr_scangle_it5.2514.5351
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.91→1.957 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 31 -
Rwork0.196 583 -
obs--86.85 %

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