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- PDB-2gf0: The crystal structure of the human DiRas1 GTPase in the inactive ... -

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Basic information

Entry
Database: PDB / ID: 2gf0
TitleThe crystal structure of the human DiRas1 GTPase in the inactive GDP bound state
ComponentsGTP-binding protein Di-Ras1
KeywordsTRANSPORT PROTEIN / DIRAS / GDP/GTP binding / GTP hydrolysis / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


GDP binding / GTPase activity / GTP binding / signal transduction / plasma membrane
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / 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 / GTP-binding protein Di-Ras1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTurnbull, A.P. / Papagrigoriou, E. / Yang, X. / Schoch, G. / Elkins, J. / Gileadi, O. / Salah, E. / Bray, J. / Wen-Hwa, L. / Fedorov, O. ...Turnbull, A.P. / Papagrigoriou, E. / Yang, X. / Schoch, G. / Elkins, J. / Gileadi, O. / Salah, E. / Bray, J. / Wen-Hwa, L. / Fedorov, O. / Niesen, F.E. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Doyle, D. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The crystal structure of the human DiRas1 GTPase in the inactive GDP bound state
Authors: Turnbull, A.P. / Papagrigoriou, E. / Yang, X. / Schoch, G. / Elkins, J. / Gileadi, O. / Salah, E. / Bray, J. / Wen-Hwa, L. / Fedorov, O. / Niesen, F.E. / von Delft, F. / Weigelt, J. / ...Authors: Turnbull, A.P. / Papagrigoriou, E. / Yang, X. / Schoch, G. / Elkins, J. / Gileadi, O. / Salah, E. / Bray, J. / Wen-Hwa, L. / Fedorov, O. / Niesen, F.E. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Doyle, D.
History
DepositionMar 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr2_label_alt_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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: GTP-binding protein Di-Ras1
B: GTP-binding protein Di-Ras1
C: GTP-binding protein Di-Ras1
D: GTP-binding protein Di-Ras1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,65312
Polymers89,7834
Non-polymers1,8708
Water10,881604
1
A: GTP-binding protein Di-Ras1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9133
Polymers22,4461
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP-binding protein Di-Ras1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9133
Polymers22,4461
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GTP-binding protein Di-Ras1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9133
Polymers22,4461
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GTP-binding protein Di-Ras1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9133
Polymers22,4461
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.053, 94.031, 61.214
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22C
32D
42B
52C
62D
72B
82C
92D
13C
23D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPARGARG5BB7 - 1708 - 171
211ASPASPARGARG5AA7 - 1708 - 171
112ASPASPGLYGLY5BB7 - 308 - 31
212ASPASPGLYGLY5CC7 - 308 - 31
312ASPASPGLYGLY5DD7 - 308 - 31
422THRTHRASPASP5BB43 - 6144 - 62
522THRTHRASPASP5CC43 - 6144 - 62
622THRTHRASPASP5DD43 - 6144 - 62
732ALAALAARGARG5BB70 - 17071 - 171
832ALAALAARGARG5CC70 - 17071 - 171
932ALAALAARGARG5DD70 - 17071 - 171
113GLYGLYASPASP1CC30 - 4231 - 43
213GLYGLYASPASP1DD30 - 4231 - 43

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
GTP-binding protein Di-Ras1 / Distinct subgroup of the Ras family member 1 / Ras-related inhibitor of cell growth / Rig protein / ...Distinct subgroup of the Ras family member 1 / Ras-related inhibitor of cell growth / Rig protein / Small GTP-binding tumor suppressor 1


Mass: 22445.834 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DIRAS1, GBTS1, RIG / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)R3 / References: UniProt: O95057
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / 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.: 4 / 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.: 604 / 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: 2.05 Å3/Da / Density % sol: 40.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3.5 M Sodium formate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9789 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 4, 2006
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 55909 / Num. obs: 55909 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.97 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ERX

2erx


Resolution: 1.9→47.09 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.94 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20781 1661 3 %RANDOM
Rwork0.15987 ---
all0.16128 54127 --
obs0.16128 54127 97.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.224 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20.02 Å2
2--0.08 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5447 0 116 620 6183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225666
X-RAY DIFFRACTIONr_bond_other_d0.0030.023791
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.9867696
X-RAY DIFFRACTIONr_angle_other_deg0.92239307
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7635708
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26824.711242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.626151038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.111532
X-RAY DIFFRACTIONr_chiral_restr0.0830.2903
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026160
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021108
X-RAY DIFFRACTIONr_nbd_refined0.2130.21053
X-RAY DIFFRACTIONr_nbd_other0.2030.23983
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22773
X-RAY DIFFRACTIONr_nbtor_other0.0830.22914
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.2499
X-RAY DIFFRACTIONr_metal_ion_refined0.0220.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.236
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2760.2136
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.260
X-RAY DIFFRACTIONr_mcbond_it2.66733765
X-RAY DIFFRACTIONr_mcbond_other0.79431408
X-RAY DIFFRACTIONr_mcangle_it3.20455629
X-RAY DIFFRACTIONr_scbond_it5.06772443
X-RAY DIFFRACTIONr_scangle_it7.049112055
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
31C163tight positional0.10.05
11B960medium positional0.040.5
21B843medium positional0.20.5
22C843medium positional0.110.5
23D843medium positional0.110.5
11B1147loose positional0.315
21B1007loose positional0.695
22C1007loose positional0.435
23D1007loose positional0.515
31C163tight thermal0.9510
11B960medium thermal0.542
21B843medium thermal0.852
22C843medium thermal0.632
23D843medium thermal0.682
11B1147loose thermal1.2410
21B1007loose thermal2.6610
22C1007loose thermal1.8910
23D1007loose thermal1.8910
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 127 -
Rwork0.228 4010 -
obs--99.28 %

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