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- PDB-5my3: Crystal structure of the RhoGAP domain of Rgd1p at 2.19 Angstroms... -

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Basic information

Entry
Database: PDB / ID: 5my3
TitleCrystal structure of the RhoGAP domain of Rgd1p at 2.19 Angstroms resolution
ComponentsRHO GTPase-activating protein RGD1
KeywordsCELL CYCLE / RhoGAP / RGD1 / polarized growth / cytokinesis
Function / homology
Function and homology information


: / : / RHOF GTPase cycle / CDC42 GTPase cycle / RHOD GTPase cycle / RHOV GTPase cycle / RHOA GTPase cycle / cellular bud / prospore membrane / actin cortical patch ...: / : / RHOF GTPase cycle / CDC42 GTPase cycle / RHOD GTPase cycle / RHOV GTPase cycle / RHOA GTPase cycle / cellular bud / prospore membrane / actin cortical patch / phosphatidylinositol-5-phosphate binding / mating projection tip / phosphatidylinositol-3-phosphate binding / response to acidic pH / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / response to osmotic stress / Neutrophil degranulation / phosphatidylinositol-4,5-bisphosphate binding / GTPase activator activity / signal transduction / identical protein binding / cytoplasm
Similarity search - Function
Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain ...Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR 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 RGD1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.19 Å
AuthorsMartinez, D.M. / d'Estaintot, B.L. / Granier, T. / Hugues, M. / Odaert, B. / Gallois, B. / Doignon, F.
CitationJournal: Biochem. J. / Year: 2017
Title: Structural evidence of a phosphoinositide-binding site in the Rgd1-RhoGAP domain.
Authors: Martinez, D. / Langlois d'Estaintot, B. / Granier, T. / Tolchard, J. / Courreges, C. / Prouzet-Mauleon, V. / Hugues, M. / Gallois, B. / Doignon, F. / Odaert, B.
History
DepositionJan 25, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionJan 24, 2018ID: 4U3K
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 RGD1


Theoretical massNumber of molelcules
Total (without water)25,7241
Polymers25,7241
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.230, 63.230, 99.730
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein RHO GTPase-activating protein RGD1 / RhoGAP / Related GAP domain protein 1


Mass: 25723.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: RGD1, YBR260C, YBR1728 / Plasmid: PET21A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P38339
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.24 Å3/Da / Density % sol: 45.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.56 / Details: HEPES, PEG3350, NAN3, TRIS, DTT, PH 7.56 / PH range: 7.2-7.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 4, 2014
RadiationMonochromator: SILICON 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.19→54.76 Å / Num. obs: 11616 / % possible obs: 99.6 % / Redundancy: 13.52 % / Biso Wilson estimate: 49.97 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.062 / Rsym value: 0.041 / Net I/σ(I): 25.57
Reflection shellResolution: 2.19→2.25 Å / Redundancy: 13.28 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.29 / Num. unique obs: 1831 / CC1/2: 0.65 / Rrim(I) all: 1.06 / Rsym value: 0.78 / % possible all: 97.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U3K

4u3k
PDB Unreleased entry


Resolution: 2.19→54.76 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.953 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.175
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2022 548 4.7 %RANDOM
Rwork0.162 ---
obs0.1639 11067 99.63 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 117.58 Å2 / Biso mean: 58.73 Å2 / Biso min: 36.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å2-0 Å2
2--0.12 Å20 Å2
3----0.39 Å2
Refinement stepCycle: final / Resolution: 2.19→54.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1601 0 0 52 1653
Biso mean---58.9 -
Num. residues----206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01916601
X-RAY DIFFRACTIONr_bond_other_d00.0215391
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.96522641
X-RAY DIFFRACTIONr_angle_other_deg3.697335821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.47952111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.2225.205731
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.392152811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2581561
X-RAY DIFFRACTIONr_chiral_restr0.0840.22621
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02118351
X-RAY DIFFRACTIONr_gen_planes_other0.0070.023071
LS refinement shellResolution: 2.19→2.246 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.293 23 3 %
Rwork0.248 777 -
obs--95.24 %
Refinement TLS params.Method: refined / Origin x: -30.373 Å / Origin y: 7.271 Å / Origin z: 16.578 Å
111213212223313233
T0.0625 Å20.0008 Å2-0.0314 Å2-0.0429 Å20.0018 Å2--0.0259 Å2
L1.521 °20.33 °2-0.3203 °2-4.8005 °20.187 °2--1.5586 °2
S0.0477 Å °0.1171 Å °-0.0897 Å °-0.1413 Å °-0.1942 Å °0.1283 Å °-0.0868 Å °0.1505 Å °0.1464 Å °

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