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- PDB-8oul: Arf GTPase from the asgard Hodarchaea : HodArfR1 bound to GDP -

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Basic information

Entry
Database: PDB / ID: 8oul
TitleArf GTPase from the asgard Hodarchaea : HodArfR1 bound to GDP
ComponentsArf GTPase
KeywordsSIGNALING PROTEIN / GTPASE / GDP / ARF FAMILY / ASGARD ARCHAEA
Function / homologyGUANOSINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesAsgard group (Asgard group)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMenetrey, J. / Jackson, C.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE13-0007 France
CitationJournal: Nat Microbiol / Year: 2025
Title: The Asgard archaeal origins of Arf family GTPases involved in eukaryotic organelle dynamics.
Authors: Vargova, R. / Chevreau, R. / Alves, M. / Courbin, C. / Terry, K. / Legrand, P. / Elias, M. / Menetrey, J. / Dacks, J.B. / Jackson, C.L.
History
DepositionApr 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification
Revision 1.2Feb 12, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arf GTPase
B: Arf GTPase
C: Arf GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7939
Polymers65,3913
Non-polymers1,4036
Water1629
1
A: Arf GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2643
Polymers21,7971
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Arf GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2643
Polymers21,7971
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Arf GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2643
Polymers21,7971
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.693, 75.693, 189.306
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 Arf GTPase


Mass: 21796.906 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Asgard group (Asgard group) / Gene: OLS23013 / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.07 Å3/Da / Density % sol: 40.68 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 4000, 0.1M Tris-HCl pH 8.5, 0.2M Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 3.1→70.3 Å / Num. obs: 10627 / % possible obs: 99.9 % / Redundancy: 18.3 % / CC1/2: 0.994 / Rrim(I) all: 0.048 / Net I/σ(I): 6.2
Reflection shellResolution: 3.1→3.29 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1678 / CC1/2: 0.063 / Rrim(I) all: 0.269 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (20-OCT-2021)refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→48.47 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.864 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.635
RfactorNum. reflection% reflectionSelection details
Rfree0.2893 459 4.96 %RANDOM
Rwork0.2364 ---
obs0.239 9259 87.1 %-
Displacement parametersBiso mean: 60.99 Å2
Baniso -1Baniso -2Baniso -3
1-2.393 Å20 Å20 Å2
2--2.393 Å20 Å2
3----4.786 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: LAST / Resolution: 3.1→48.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4139 0 87 9 4235
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094316HARMONIC2
X-RAY DIFFRACTIONt_angle_deg15891HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1418SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes762HARMONIC5
X-RAY DIFFRACTIONt_it4316HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.51
X-RAY DIFFRACTIONt_other_torsion20.42
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion605SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3360SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 23
RfactorNum. reflection% reflection
Rfree0.3892 -3.56 %
Rwork0.2771 406 -
all0.2808 421 -
obs--53.11 %

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