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- PDB-5wdr: Choanoflagellate Salpingoeca rosetta Ras with GMP-PNP -

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Basic information

Entry
Database: PDB / ID: 5wdr
TitleChoanoflagellate Salpingoeca rosetta Ras with GMP-PNP
ComponentsRas protein
KeywordsONCOPROTEIN / HYDROLASE / small G-protein / GTPase
Function / homology
Function and homology information


GTPase activity / GTP binding / signal transduction / metal ion binding / membrane
Similarity search - Function
Small GTPase Rab domain profile. / Small GTPase Rho domain profile. / Small GTPase, Ras-type / Small GTPase Ras domain 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 ...Small GTPase Rab domain profile. / Small GTPase Rho domain profile. / Small GTPase, Ras-type / Small GTPase Ras domain 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras protein
Similarity search - Component
Biological speciesSalpingoeca rosetta (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKondo, Y. / Gee, C.L. / Kuriyan, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI091580 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2017
Title: Deconstruction of the Ras switching cycle through saturation mutagenesis.
Authors: Bandaru, P. / Shah, N.H. / Bhattacharyya, M. / Barton, J.P. / Kondo, Y. / Cofsky, J.C. / Gee, C.L. / Chakraborty, A.K. / Kortemme, T. / Ranganathan, R. / Kuriyan, J.
History
DepositionJul 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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.ptnr1_symmetry / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras protein
B: Ras protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1558
Polymers39,0162
Non-polymers1,1396
Water3,387188
1
A: Ras protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0774
Polymers19,5081
Non-polymers5693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0774
Polymers19,5081
Non-polymers5693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.562, 119.106, 38.570
Angle α, β, γ (deg.)90.00, 117.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ras protein


Mass: 19507.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salpingoeca rosetta (eukaryote) / Gene: PTSG_05504 / Plasmid: pProEX HTb / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F2UBE5, small monomeric GTPase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.02 Å3/Da / Density % sol: 39.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 15 % PEG8000, 100 mM Bis-Tris, pH 5.5, 200 mM magnesium acetate, 50 mM calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2015
Details: Pt/Rh coated collimating and toroid focusing mirrors
RadiationMonochromator: Kohzu: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 1.6→39.7 Å / Num. obs: 40589 / % possible obs: 99.9 % / Redundancy: 4.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.047 / Net I/σ(I): 9.5
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.944 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1969 / CC1/2: 0.428 / Rpim(I) all: 0.557 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5WDS

5wds


Resolution: 1.6→34.261 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.08
RfactorNum. reflection% reflection
Rfree0.2798 2065 5.09 %
Rwork0.2285 --
obs0.231 40549 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→34.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2684 0 68 188 2940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112872
X-RAY DIFFRACTIONf_angle_d1.2343902
X-RAY DIFFRACTIONf_dihedral_angle_d21.6351750
X-RAY DIFFRACTIONf_chiral_restr0.062429
X-RAY DIFFRACTIONf_plane_restr0.007502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.63720.36711370.32497X-RAY DIFFRACTION100
1.6372-1.67820.35311340.2812634X-RAY DIFFRACTION100
1.6782-1.72360.30351230.26822496X-RAY DIFFRACTION100
1.7236-1.77430.36391640.27052551X-RAY DIFFRACTION100
1.7743-1.83150.33871750.26462549X-RAY DIFFRACTION100
1.8315-1.8970.27851430.26372531X-RAY DIFFRACTION100
1.897-1.97290.2791400.23612558X-RAY DIFFRACTION100
1.9729-2.06270.32081190.23462601X-RAY DIFFRACTION100
2.0627-2.17140.28061820.22842504X-RAY DIFFRACTION100
2.1714-2.30750.25681410.21522578X-RAY DIFFRACTION100
2.3075-2.48560.27991150.2122579X-RAY DIFFRACTION100
2.4856-2.73560.26841200.22342615X-RAY DIFFRACTION100
2.7356-3.13120.25711310.22132585X-RAY DIFFRACTION100
3.1312-3.94410.24171050.21462591X-RAY DIFFRACTION100
3.9441-34.26850.25591360.21032615X-RAY DIFFRACTION100

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