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- PDB-5u4u: pseudoGTPase domain (pG1) of p190RhoGAP-A -

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Basic information

Entry
Database: PDB / ID: 5u4u
TitlepseudoGTPase domain (pG1) of p190RhoGAP-A
ComponentsMGC81300 protein
KeywordsHYDROLASE / GTPase / pseudoGTPase / G domain / Rho / GAP / ARHGAP5 / ARHGAP35
Function / homology
Function and homology information


GTPase activator activity / cell projection / positive regulation of GTPase activity / cytoskeleton / GTPase activity / lipid binding / GTP binding / signal transduction / nucleus / plasma membrane / cytoplasm
Similarity search - Function
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. ...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 / Small GTPase / Ras family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
MALONATE ION / Uncharacterized protein / Rho GTPase-activating protein 35
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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

Downloads & links

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Assembly

Deposited unit
A: MGC81300 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0916
Polymers19,8181
Non-polymers2735
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.937, 62.937, 161.017
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein MGC81300 protein / p190RhoGAP-A


Mass: 19817.523 Da / Num. of mol.: 1 / Fragment: UNP residues 587-762
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: arhgap35, MGC81300 / Plasmid: pET32 modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6NU25, UniProt: A0A1L8F832*PLUS
#2: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 1.7-1.8 M Lithium Sulfate, 0.1 M N-(2-Acetamido)iminodiacetic acid (ADA)

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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: Apr 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 15922 / % possible obs: 99.7 % / Redundancy: 8.9 % / Rsym value: 0.018 / Net I/σ(I): 11.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 1.5 / CC1/2: 0.3 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IHW

3ihw


Resolution: 1.9→45.13 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.17
RfactorNum. reflection% reflectionSelection details
Rfree0.217 802 5.1 %RANDOM
Rwork0.181 ---
obs0.183 15634 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.84 Å2 / Biso mean: 33.856 Å2 / Biso min: 11.93 Å2
Refinement stepCycle: final / Resolution: 1.9→45.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1230 0 17 81 1328
Biso mean--42.26 42.73 -
Num. residues----157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071323
X-RAY DIFFRACTIONf_angle_d0.9521789
X-RAY DIFFRACTIONf_chiral_restr0.043209
X-RAY DIFFRACTIONf_plane_restr0.003237
X-RAY DIFFRACTIONf_dihedral_angle_d11.641512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-2.01920.35751170.27662393X-RAY DIFFRACTION100
2.0192-2.17510.27181450.20772408X-RAY DIFFRACTION100
2.1751-2.39390.25241170.17882424X-RAY DIFFRACTION100
2.3939-2.74030.20141440.18052452X-RAY DIFFRACTION100
2.7403-3.45230.21291310.17042492X-RAY DIFFRACTION100
3.4523-45.10.18361480.16642663X-RAY DIFFRACTION100
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)
19.6897-1.375-2.38712.43980.6693.8455-0.2970.4448-0.61980.01520.1765-0.01020.4930.0517-0.04260.1822-0.02340.01560.11530.00210.1491-14.86231.40614.1563
22.92871.095-0.50222.6424-0.97183.257-0.08750.0356-0.3451-0.218-0.0167-0.18170.49670.01520.05820.26760.00550.01790.1512-0.02650.2447-18.310531.15692.5099
33.78790.8641-1.16372.45350.30464.1395-0.11350.2170.0864-0.02040.02770.19030.0923-0.28610.0070.1268-0.0340.00650.174-0.0050.1887-28.249538.543914.1944
41.8116-1.44692.01952.811-0.89365.30160.0775-0.0988-0.1367-0.01260.0284-0.24130.51650.21670.03380.23710.012-0.00290.1784-0.00370.2644-9.974738.342111.324
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 586 through 602 )A586 - 602
2X-RAY DIFFRACTION2chain 'A' and (resid 603 through 654 )A603 - 654
3X-RAY DIFFRACTION3chain 'A' and (resid 655 through 742 )A655 - 742
4X-RAY DIFFRACTION4chain 'A' and (resid 743 through 762 )A743 - 762

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