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- PDB-8ouk: Arf GTPase from the asgard Hodarchaea : HodArfR1 bound to GTP -

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Basic information

Entry
Database: PDB / ID: 8ouk
TitleArf GTPase from the asgard Hodarchaea : HodArfR1 bound to GTP
ComponentsArf GTPase
KeywordsSIGNALING PROTEIN / Arf GTPases / Asgaard Archaea
Function / homology
Function and homology information


GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Small GTPase superfamily, ARF type / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Mutual gliding-motility protein MglA
Similarity search - Component
Biological speciesAsgard group (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMenetrey, J. / Jackson, C. / Dacks, J. / Elias, M. / Vargova, R.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE13-0007-02 France
CitationJournal: To Be Published
Title: Arf Family GTPases are present in Asgard archaea
Authors: Menetrey, J. / Jackson, C.
History
DepositionApr 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arf GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7603
Polymers20,2131
Non-polymers5472
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-15 kcal/mol
Surface area8580 Å2
Unit cell
Length a, b, c (Å)59.120, 59.120, 119.730
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: 20213.002 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Asgard group (archaea) / Gene: OLS23013 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q9NLL0
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#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


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.59 Å3/Da / Density % sol: 52.47 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.0 M Sodium formate and 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.979415 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979415 Å / Relative weight: 1
ReflectionResolution: 1.8→42.1 Å / Num. obs: 20387 / % possible obs: 99 % / Redundancy: 20 % / CC1/2: 1 / Rrim(I) all: 0.044 / Net I/σ(I): 39.8
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 1982 / CC1/2: 0.981 / Rrim(I) all: 0.582

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Processing

Software
NameClassification
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→18.72 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.118 / SU Rfree Blow DPI: 0.108 / SU Rfree Cruickshank DPI: 0.105
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1010 4.95 %RANDOM
Rwork0.1923 ---
obs0.1934 20387 99.9 %-
Displacement parametersBiso mean: 42.95 Å2
Baniso -1Baniso -2Baniso -3
1--7.5865 Å20 Å20 Å2
2---7.5865 Å20 Å2
3---15.173 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.8→18.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1377 0 33 97 1507
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081440HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.91962HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d499SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes251HARMONIC5
X-RAY DIFFRACTIONt_it1440HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.62
X-RAY DIFFRACTIONt_other_torsion15.62
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion192SEMIHARMONIC5
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_contact1227SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.81 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.28 -5.15 %
Rwork0.1927 387 -
all0.1965 408 -
obs--99.76 %
Refinement TLS params.Method: refined / Origin x: 4.691 Å / Origin y: -27.7471 Å / Origin z: 4.6504 Å
111213212223313233
T0.3014 Å20.0103 Å20.0009 Å2-0.3166 Å2-0.0069 Å2--0.2893 Å2
L0.8931 °2-0.0125 °2-0.0387 °2-1.395 °2-0.6807 °2--4.7999 °2
S0.057 Å °-0.0456 Å °0.0567 Å °0.0011 Å °-0.0553 Å °-0.0022 Å °-0.112 Å °0.0131 Å °-0.0018 Å °
Refinement TLS groupSelection details: { *|* }

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