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- PDB-5xgc: Crystal structure of SmgGDS-558 -

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Basic information

Entry
Database: PDB / ID: 5xgc
TitleCrystal structure of SmgGDS-558
ComponentsRap1 GTPase-GDP dissociation stimulator 1
KeywordsONCOPROTEIN / armadillo GEF
Function / homology
Function and homology information


regulation of ERK5 cascade / CAAX-box protein maturation / angiotensin-activated signaling pathway involved in heart process / RHOT1 GTPase cycle / RHOT2 GTPase cycle / regulation of matrix metallopeptidase secretion / vascular associated smooth muscle contraction / myosin filament assembly / positive regulation of mitochondrial calcium ion concentration / negative regulation of endoplasmic reticulum calcium ion concentration ...regulation of ERK5 cascade / CAAX-box protein maturation / angiotensin-activated signaling pathway involved in heart process / RHOT1 GTPase cycle / RHOT2 GTPase cycle / regulation of matrix metallopeptidase secretion / vascular associated smooth muscle contraction / myosin filament assembly / positive regulation of mitochondrial calcium ion concentration / negative regulation of endoplasmic reticulum calcium ion concentration / cardiac muscle hypertrophy / regulation of mitochondrion organization / negative regulation of GTPase activity / protein localization to nucleus / guanyl-nucleotide exchange factor activity / positive regulation of GTPase activity / endoplasmic reticulum / mitochondrion / extracellular exosome / nucleus / cytosol
Similarity search - Function
Rap1 GTPase-GDP dissociation stimulator 1 / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Rap1 GTPase-GDP dissociation stimulator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsShimizu, H. / Toma-Fukai, S. / Shimizu, T.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structure-based analysis of the guanine nucleotide exchange factor SmgGDS reveals armadillo-repeat motifs and key regions for activity and GTPase binding
Authors: Shimizu, H. / Toma-Fukai, S. / Saijo, S. / Shimizu, N. / Kontani, K. / Katada, T. / Shimizu, T.
History
DepositionApr 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed
Revision 1.2Aug 23, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Rap1 GTPase-GDP dissociation stimulator 1


Theoretical massNumber of molelcules
Total (without water)55,0351
Polymers55,0351
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22000 Å2
Unit cell
Length a, b, c (Å)194.330, 51.115, 52.444
Angle α, β, γ (deg.)90.00, 92.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Rap1 GTPase-GDP dissociation stimulator 1 / Exchange factor smgGDS / SMG GDS protein / SMG P21 stimulatory GDP/GTP exchange protein


Mass: 55034.820 Da / Num. of mol.: 1 / Fragment: UNP residues 61-558
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAP1GDS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52306
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: PEG 3,350, MgCl2, HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 32018 / % possible obs: 99.9 % / Redundancy: 10.9 % / Rpim(I) all: 0.029 / Net I/σ(I): 47.7
Reflection shellResolution: 2.07→2.11 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 2.4 / CC1/2: 0.79 / Rpim(I) all: 0.459 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→49.43 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.159 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.189 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25156 1546 5.1 %RANDOM
Rwork0.21461 ---
obs0.2166 28726 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 64.592 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.02 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.1→49.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3458 0 0 74 3532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193491
X-RAY DIFFRACTIONr_bond_other_d0.0010.023555
X-RAY DIFFRACTIONr_angle_refined_deg1.2391.9734726
X-RAY DIFFRACTIONr_angle_other_deg0.80638146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0175471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.51226.231130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30115620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8671512
X-RAY DIFFRACTIONr_chiral_restr0.0690.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023985
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02703
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0356.4931890
X-RAY DIFFRACTIONr_mcbond_other3.0356.4891889
X-RAY DIFFRACTIONr_mcangle_it4.4329.7192359
X-RAY DIFFRACTIONr_mcangle_other4.4319.7232360
X-RAY DIFFRACTIONr_scbond_it3.5466.4361601
X-RAY DIFFRACTIONr_scbond_other3.5456.441602
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4399.5952368
X-RAY DIFFRACTIONr_long_range_B_refined7.47850.3324082
X-RAY DIFFRACTIONr_long_range_B_other7.47450.354076
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 111 -
Rwork0.308 2089 -
obs--99.68 %

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