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- PDB-1rgp: GTPASE-ACTIVATION DOMAIN FROM RHOGAP -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1rgp
TitleGTPASE-ACTIVATION DOMAIN FROM RHOGAP
ComponentsRHOGAPRhoGAP domain
KeywordsG-PROTEIN / GAP / SIGNAL-TRANSDUCTION
Function / homology
Function and homology information


negative regulation of endocytic recycling / transferrin transport / RHOF GTPase cycle / RHOD GTPase cycle / regulation of small GTPase mediated signal transduction / RND2 GTPase cycle / endosomal transport / RHOB GTPase cycle / small GTPase-mediated signal transduction / RHOJ GTPase cycle ...negative regulation of endocytic recycling / transferrin transport / RHOF GTPase cycle / RHOD GTPase cycle / regulation of small GTPase mediated signal transduction / RND2 GTPase cycle / endosomal transport / RHOB GTPase cycle / small GTPase-mediated signal transduction / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / Rho protein signal transduction / RHOG GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / RAC1 GTPase cycle / GTPase activator activity / small GTPase binding / SH3 domain binding / endosome membrane / cadherin binding / perinuclear region of cytoplasm / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
: / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Divergent CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain ...: / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Divergent CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Rho GTPase-activating protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR/MAD / Resolution: 2 Å
AuthorsBarrett, T. / Xiao, B. / Dodson, E.J. / Dodson, G. / Ludbrook, S.B. / Nurmahomed, K. / Gamblin, S.J. / Musacchio, A. / Smerdon, S.J. / Eccleston, J.F.
CitationJournal: Nature / Year: 1997
Title: The structure of the GTPase-activating domain from p50rhoGAP.
Authors: Barrett, T. / Xiao, B. / Dodson, E.J. / Dodson, G. / Ludbrook, S.B. / Nurmahomed, K. / Gamblin, S.J. / Musacchio, A. / Smerdon, S.J. / Eccleston, J.F.
History
DepositionDec 5, 1996Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RHOGAP


Theoretical massNumber of molelcules
Total (without water)27,4441
Polymers27,4441
Non-polymers00
Water4,702261
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.086, 70.086, 79.205
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 RHOGAP / RhoGAP domain / CDC42 GTPASE-ACTIVATING PROTEIN


Mass: 27444.469 Da / Num. of mol.: 1 / Fragment: GTPASE ACTIVATION DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: Q07960
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.4 Å3/Da / Density % sol: 45 %
Crystal growpH: 7.5 / Details: 10% PEG 6K, 5% MPD IN 0.1M HEPES PH 7.5
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %PEG60001reservoir
25 %MPD1reservoir
30.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 14248 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 10.3
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.38 / % possible all: 95

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Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MIR/MAD / Resolution: 2→20 Å / Cross valid method: FREE R / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.283 -5 %
Rwork0.22 --
obs-14234 99.6 %
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1770 0 0 269 2039
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.22 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_deg1.8

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