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- PDB-2g3y: Crystal structure of the human small GTPase GEM -

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Basic information

Entry
Database: PDB / ID: 2g3y
TitleCrystal structure of the human small GTPase GEM
ComponentsGTP-binding protein GEM
KeywordsSIGNALING PROTEIN / GEM / small GTPase / GDP / inactive state / RGK family / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


metaphase chromosome alignment / calcium channel regulator activity / chromosome organization / spindle midzone / NPAS4 regulates expression of target genes / cytoplasmic side of plasma membrane / mitotic spindle / GDP binding / mitotic cell cycle / midbody ...metaphase chromosome alignment / calcium channel regulator activity / chromosome organization / spindle midzone / NPAS4 regulates expression of target genes / cytoplasmic side of plasma membrane / mitotic spindle / GDP binding / mitotic cell cycle / midbody / cell surface receptor signaling pathway / calmodulin binding / immune response / GTPase activity / GTP binding / magnesium ion binding / signal transduction / nucleus / plasma membrane
Similarity search - Function
Ras-related small G protein, RGK family / small GTPase Ras family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...Ras-related small G protein, RGK family / small GTPase Ras family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GTP-binding protein GEM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsUgochukwu, E. / Soundararajan, M. / Elkins, J. / Gileadi, C. / Schoch, G. / Sobott, F. / Fedorov, O. / Bray, J. / Pantic, N. / Berridge, G. ...Ugochukwu, E. / Soundararajan, M. / Elkins, J. / Gileadi, C. / Schoch, G. / Sobott, F. / Fedorov, O. / Bray, J. / Pantic, N. / Berridge, G. / Burgess, N. / Lee, W.H. / Turnbull, A. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / von Delft, F. / Doyle, D. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the human small GTPase GEM
Authors: Ugochukwu, E. / Soundararajan, M. / Elkins, J. / Schoch, G. / Gileadi, C. / Doyle, D.
History
DepositionFeb 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTP-binding protein GEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2982
Polymers23,8551
Non-polymers4431
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.242, 51.242, 173.873
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein GTP-binding protein GEM / GTP-binding mitogen-induced T-cell protein / RAS-like protein KIR


Mass: 23854.738 Da / Num. of mol.: 1 / Fragment: GEM
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GEM, KIR / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)-R3 / References: UniProt: P55040
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PEG3350, Ammonium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 11803 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.25→2.37 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RAP, 1KAO

2rap

1kao


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.909 / SU B: 15.649 / SU ML: 0.195 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.32 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26925 463 4.7 %RANDOM
Rwork0.21803 ---
all0.22039 9339 --
obs0.22039 9339 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2--0.9 Å20 Å2
3----1.8 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1306 0 28 35 1369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211366
X-RAY DIFFRACTIONr_bond_other_d0.0020.02889
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.9681856
X-RAY DIFFRACTIONr_angle_other_deg0.89732156
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3655171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4323.84665
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.41515228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1521512
X-RAY DIFFRACTIONr_chiral_restr0.070.2213
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021532
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02286
X-RAY DIFFRACTIONr_nbd_refined0.1860.2272
X-RAY DIFFRACTIONr_nbd_other0.1920.2947
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2664
X-RAY DIFFRACTIONr_nbtor_other0.0850.2758
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.246
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.070.24
X-RAY DIFFRACTIONr_mcbond_it0.531.5859
X-RAY DIFFRACTIONr_mcbond_other0.091.5350
X-RAY DIFFRACTIONr_mcangle_it0.93821349
X-RAY DIFFRACTIONr_scbond_it1.3733578
X-RAY DIFFRACTIONr_scangle_it2.1094.5506
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 34 -
Rwork0.299 663 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -6.7295 Å / Origin y: 3.5538 Å / Origin z: -15.5265 Å
111213212223313233
T-0.0002 Å20.0088 Å2-0.1645 Å2--0.3711 Å20.0091 Å2---0.2275 Å2
L3.0674 °2-0.7026 °22.5713 °2-5.5518 °2-0.8753 °2--8.6807 °2
S-0.0641 Å °0.2096 Å °-0.1407 Å °-0.5992 Å °-0.1801 Å °0.026 Å °-0.5206 Å °0.2601 Å °0.2442 Å °

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