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- PDB-2ery: The crystal structure of the Ras related protein RRas2 (RRAS2) in... -

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Basic information

Entry
Database: PDB / ID: 2ery
TitleThe crystal structure of the Ras related protein RRas2 (RRAS2) in the GDP bound state
ComponentsRas-related protein R-Ras2
KeywordsSIGNALING PROTEIN / RRAS2 / GDP/GTP binding / GTP hydrolysis / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


: / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / osteoblast differentiation / GDP binding / Ras protein signal transduction / positive regulation of cell migration / Golgi membrane / focal adhesion / GTPase activity / GTP binding ...: / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / osteoblast differentiation / GDP binding / Ras protein signal transduction / positive regulation of cell migration / Golgi membrane / focal adhesion / GTPase activity / GTP binding / endoplasmic reticulum / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / Small GTPase / Ras family / 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 / Ras-related protein R-Ras2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSalah, E. / Schoch, G. / Turnbull, A. / Papagrigoriou, E. / Soundararajan, M. / Burgess, N. / Elkins, J. / Gileadi, C. / Gileadi, O. / von Delft, F. ...Salah, E. / Schoch, G. / Turnbull, A. / Papagrigoriou, E. / Soundararajan, M. / Burgess, N. / Elkins, J. / Gileadi, C. / Gileadi, O. / von Delft, F. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / Sundstrom, M. / Doyle, D. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The crystal structure of the Ras related protein RRas2 (RRAS2) in the GDP bound state
Authors: Salah, E. / Schoch, G. / Turnbull, A. / Papagrigoriou, E. / Soundararajan, M. / Burgess, N. / Elkins, J. / Gileadi, C. / Gileadi, O. / von Delft, F. / Edwards, A. / Arrowsmith, C. / Weigelt, ...Authors: Salah, E. / Schoch, G. / Turnbull, A. / Papagrigoriou, E. / Soundararajan, M. / Burgess, N. / Elkins, J. / Gileadi, C. / Gileadi, O. / von Delft, F. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / Sundstrom, M. / Doyle, D.
History
DepositionOct 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein R-Ras2
B: Ras-related protein R-Ras2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8786
Polymers39,9432
Non-polymers9354
Water5,224290
1
A: Ras-related protein R-Ras2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4393
Polymers19,9721
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related protein R-Ras2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4393
Polymers19,9721
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.191, 72.115, 82.073
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 6

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUALAALAAA13 - 704 - 61
21GLUGLUALAALABB13 - 704 - 61
12TYRTYRGLUGLUAA82 - 18073 - 171
22TYRTYRGLUGLUBB82 - 18073 - 171

NCS ensembles :
ID
1
2

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Components

#1: Protein Ras-related protein R-Ras2 / Ras-like protein TC21 / Teratocarcinoma oncogene


Mass: 19971.627 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RRAS2, TC21 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3)R3 / References: UniProt: P62070
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 277 K / pH: 5.5
Details: 8 % PEG3350, 0.005 M MgCl2, 0.005 M CoCl2, 0.1 M Bis Tris, 0.1 M Mg(Formate)2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 5.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99989
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 1, 2005
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99989 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 40966 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 5.8 %
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.5 % / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1X1R.PDB

1x1r


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.384 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2062 5 %RANDOM
Rwork0.196 ---
obs0.198 38848 98.9 %-
all-38848 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.16 Å2
Baniso -1Baniso -2Baniso -3
1--2 Å20 Å20 Å2
2--3.24 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2688 0 58 290 3036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222836
X-RAY DIFFRACTIONr_bond_other_d0.0010.022600
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.9783824
X-RAY DIFFRACTIONr_angle_other_deg1.57535997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9115337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.77523.378148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63615519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3281530
X-RAY DIFFRACTIONr_chiral_restr0.150.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023127
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02627
X-RAY DIFFRACTIONr_nbd_refined0.1930.2534
X-RAY DIFFRACTIONr_nbd_other0.1790.22792
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21388
X-RAY DIFFRACTIONr_nbtor_other0.0830.21747
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2201
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0290.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6931.51749
X-RAY DIFFRACTIONr_mcbond_other0.1621.5697
X-RAY DIFFRACTIONr_mcangle_it0.99722690
X-RAY DIFFRACTIONr_scbond_it1.57531275
X-RAY DIFFRACTIONr_scangle_it2.2924.51132
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1793loose positional1.295
21396loose positional0.475
1793loose thermal1.1510
21396loose thermal0.8610
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 173 -
Rwork0.219 2548 -
obs--90.28 %
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)
14.34580.77530.23080.9035-0.21355.03930.01070.0763-0.17050.0819-0.0464-0.1524-0.0615-0.12990.03570.05150.00450.0261-0.05930.01090.057810.98064.11654.4665
22.42930.0495-0.07090.6122-0.18663.86560.01250.1553-0.0147-0.02350.01120.0068-0.09130.0455-0.02370.0294-0.00930.0068-0.02590.02230.048710.53321.92291.4539
35.80860.51892.23731.10360.11942.98960.0270.2764-0.0910.04930.0154-0.0275-0.05970.2491-0.04240.00830.00380.00230.01730.02740.03099.18192.4384.5989
42.57920.54170.12171.16570.20074.5240.0220.06890.04360.0816-0.026-0.0243-0.1599-0.06190.0040.01270.0067-0.0002-0.01070.01980.040711.06952.31534.2519
54.73530.47340.51761.32171.33594.0982-0.02020.08460.0826-0.1258-0.1040.0956-0.2261-0.08530.12420.05770.0267-0.02970.02630.0360.1095-18.5258-5.5036-6.065
63.81590.12790.1130.7865-0.2371.76430.00510.075-0.00240.0297-0.0171-0.0540.05810.12590.0120.00530.0283-0.00240.1030.02980.0508-16.9412-2.739-5.2904
74.6206-0.3896-1.40421.32740.44812.42780.0028-0.18880.0449-0.00560.0550.00640.04790.4072-0.0579-0.00630.0276-0.00980.19660.01870.0194-20.5889-3.8597-6.4762
85.7999-0.01271.48970.73250.20313.09030.059-0.005-0.2143-0.0787-0.0412-0.05120.0472-0.1357-0.01780.0215-0.0036-0.00920.05170.03150.0469-17.8316-3.9272-5.8076
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 51
2X-RAY DIFFRACTION2A52 - 100
3X-RAY DIFFRACTION3A101 - 133
4X-RAY DIFFRACTION4A134 - 180
5X-RAY DIFFRACTION5B25 - 55
6X-RAY DIFFRACTION6B56 - 95
7X-RAY DIFFRACTION7B96 - 142
8X-RAY DIFFRACTION8B143 - 181

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