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- PDB-5u4v: pseudoGTPase domain (pG1) of p190RhoGAP-B -

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Basic information

Entry
Database: PDB / ID: 5u4v
TitlepseudoGTPase domain (pG1) of p190RhoGAP-B
ComponentsRho GTPase-activating protein 5
KeywordsHYDROLASE / GTPase / pseudoGTPase / G domain / Rho / GAP / ARHGAP5 / ARHGAP35
Function / homology
Function and homology information


epithelial cell migration / mammary gland development / RHOF GTPase cycle / RHOD GTPase cycle / regulation of small GTPase mediated signal transduction / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of mesenchymal cell proliferation / regulation of cell size ...epithelial cell migration / mammary gland development / RHOF GTPase cycle / RHOD GTPase cycle / regulation of small GTPase mediated signal transduction / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of mesenchymal cell proliferation / regulation of cell size / RHOB GTPase cycle / positive regulation of epithelial cell migration / 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 / RAC1 GTPase cycle / SH2 domain binding / GTPase activator activity / cell adhesion / GTPase activity / endoplasmic reticulum / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Rho GTPase-activating protein, pG1 and pG2 domain / p190RhoGAP, pG1 and pG2 domains / Rho GTPase-activating protein, FF domain / Rho GTPase-activating protein, pG2 domain / Rho GTPase-activating protein, pG1 domain / p190-A and -B Rho GAPs FF domain / pG1 pseudoGTPase domain profile. / pG2 pseudoGTPase domain profile. / FF domain / FF domain ...Rho GTPase-activating protein, pG1 and pG2 domain / p190RhoGAP, pG1 and pG2 domains / Rho GTPase-activating protein, FF domain / Rho GTPase-activating protein, pG2 domain / Rho GTPase-activating protein, pG1 domain / p190-A and -B Rho GAPs FF domain / pG1 pseudoGTPase domain profile. / pG2 pseudoGTPase domain profile. / FF domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Rho GTPase-activating protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsStiegler, A.L. / Boggon, T.J.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS085078 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM109487 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM114621 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM102262 United States
National Institutes of Health/Office of the DirectorS10OD018007 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM100411 United States
CitationJournal: Nat Commun / Year: 2017
Title: p190RhoGAP proteins contain pseudoGTPase domains.
Authors: Stiegler, A.L. / Boggon, T.J.
History
DepositionDec 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho GTPase-activating protein 5


Theoretical massNumber of molelcules
Total (without water)19,8441
Polymers19,8441
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.763, 40.763, 95.214
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Rho GTPase-activating protein 5 / Rho-type GTPase-activating protein 5 / p190-B


Mass: 19843.621 Da / Num. of mol.: 1 / Fragment: UNP residues 590-763
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGAP5, RHOGAP5 / Plasmid: pET32 modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13017
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 1.99 Å3/Da / Density % sol: 38.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7 / Details: 2.15 M sodium malonate pH 4.7 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 4908 / % possible obs: 99.9 % / Redundancy: 4.1 % / Rpim(I) all: 0.066 / Net I/σ(I): 11.6
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.8 / CC1/2: 0.656 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U4U

5u4u


Resolution: 2.6→40.76 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.877 / SU B: 29.836 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.345 / ESU R Free: 0.352
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2736 240 5 %RANDOM
Rwork0.2441 ---
obs0.2456 4569 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 128.58 Å2 / Biso mean: 58.743 Å2 / Biso min: 24.99 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å20 Å2
2--1.58 Å20 Å2
3----3.16 Å2
Refinement stepCycle: final / Resolution: 2.6→40.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1075 0 0 5 1080
Biso mean---39.36 -
Num. residues----136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191089
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.9711464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2935131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74225.3754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.18215198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.198156
X-RAY DIFFRACTIONr_chiral_restr0.0990.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021804
X-RAY DIFFRACTIONr_mcbond_it1.6263.339539
X-RAY DIFFRACTIONr_mcangle_it2.5624.991665
X-RAY DIFFRACTIONr_scbond_it1.753.482550
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 14 -
Rwork0.208 350 -
all-364 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.969-1.5224-1.555.1212-1.10890.62330.019-0.33810.0133-0.3509-0.0468-0.19110.12470.03640.02780.1934-0.0879-0.01060.21250.04160.135140.471731.165350.5839
26.4531-1.62623.39620.945-1.94289.9756-0.0651-0.1329-0.4427-0.01070.0235-0.19540.34140.84380.04150.05080.06770.03850.146-0.01550.270449.087934.156852.4232
33.291-0.306-3.23859.4880.51063.7038-0.0307-0.1695-0.6044-0.3657-0.38990.45470.53430.21960.42060.54540.0325-0.16680.1198-0.05940.225729.602326.346555.6874
46.9719-0.1173-1.92844.66050.8228.23590.0479-0.09930.7724-0.1352-0.06480.3327-0.0981-0.55610.01690.0502-0.05360.02380.1236-0.0680.134734.657838.379860.2447
54.1275-0.4413-1.18360.26871.15715.1410.13230.0327-0.2047-0.01580.0831-0.0398-0.03810.4231-0.21540.18310.02930.04150.14510.0440.33547.020828.743167.4547
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A594 - 609
2X-RAY DIFFRACTION2A610 - 657
3X-RAY DIFFRACTION3A658 - 691
4X-RAY DIFFRACTION4A692 - 753
5X-RAY DIFFRACTION5A754 - 761

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