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- PDB-7eze: Thorarchaeota Rab GTP-gamma-S/Mg2+ (soak) -

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Basic information

Entry
Database: PDB / ID: 7eze
TitleThorarchaeota Rab GTP-gamma-S/Mg2+ (soak)
ComponentsThorarchaeota Rab
KeywordsSIGNALING PROTEIN / Rab / Small GTPase
Function / homology
Function and homology information


GTPase activity / GTP binding
Similarity search - Function
small GTPase Rab1 family profile. / small GTPase Rho family profile. / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / GTP-binding protein
Similarity search - Component
Biological speciesCandidatus Thorarchaeota archaeon SMTZ1-45 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsRobinson, R.C. / Tran, L.T.
Funding support Japan, United States, 3items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR19S5 Japan
Japan Society for the Promotion of Science (JSPS)JP20H00476 Japan
Moore and Simons foundationsGBMF9743 United States
CitationJournal: To Be Published
Title: Structure of Thor-Rab
Authors: Robinson, R.C. / Tran, L.T.
History
DepositionJun 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thorarchaeota Rab
B: Thorarchaeota Rab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8785
Polymers41,7752
Non-polymers1,1033
Water4,720262
1
A: Thorarchaeota Rab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4513
Polymers20,8881
Non-polymers5642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-17 kcal/mol
Surface area9130 Å2
MethodPISA
2
B: Thorarchaeota Rab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4272
Polymers20,8881
Non-polymers5391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-7 kcal/mol
Surface area9000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.133, 69.133, 66.927
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

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Components

#1: Protein Thorarchaeota Rab


Mass: 20887.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Thorarchaeota archaeon SMTZ1-45 (archaea)
Gene: AM325_13980 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A135VL07
#2: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM MES, pH 5.5, 250 mM NaCl, 13% PEG 8000, 5 mM GTP soaked with 10 mM GTP gamma-S, 15 mM MgCl2 (1 h)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 25510 / % possible obs: 97.8 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.041 / Rrim(I) all: 0.096 / Net I/σ(I): 16.7
Reflection shellResolution: 1.95→1.98 Å / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1304 / CC1/2: 0.507 / Rpim(I) all: 0.498 / Rrim(I) all: 0.964

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Processing

Software
NameVersionClassification
PHENIXv1.17.1refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EZB

7ezb


Resolution: 1.95→19.96 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2009 1264 -
Rwork0.1663 --
obs-25490 97.69 %
Displacement parametersBiso mean: 34.25 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2760 0 65 262 3087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032971
X-RAY DIFFRACTIONf_angle_d0.64254044
X-RAY DIFFRACTIONf_chiral_restr0.0442445
X-RAY DIFFRACTIONf_plane_restr0.0023517
X-RAY DIFFRACTIONf_dihedral_angle_d20.44881138
LS refinement shellResolution: 1.95→2.02 Å
RfactorNum. reflection% reflection
Rfree0.294 168 -
Rwork0.256 2590 -
obs--99.2 %

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