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- PDB-8oun: Arf GTPase from the asgard Gerdarchaea : GerdArfR1 bound to GDP -

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Basic information

Entry
Database: PDB / ID: 8oun
TitleArf GTPase from the asgard Gerdarchaea : GerdArfR1 bound to GDP
ComponentsGTP-binding protein
KeywordsSIGNALING PROTEIN / GTPASE / GDP / ARF FAMILY / ASGARD ARCHAEA / Gerdarchaea
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. / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GTP-binding protein
Similarity search - Component
Biological speciesAsgard group archaeon (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.653 Å
AuthorsMenetrey, J. / Jackson, C. / Dacks, J.B. / Elias, M. / Vargova, R.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE13-0007 France
CitationJournal: To Be Published
Title: Arf Family GTPases are present in Asgard archaea
Authors: Menetrey, J.
History
DepositionApr 24, 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: GTP-binding protein
B: GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1556
Polymers43,2202
Non-polymers9354
Water5,639313
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-39 kcal/mol
Surface area17230 Å2
Unit cell
Length a, b, c (Å)43.290, 59.930, 72.350
Angle α, β, γ (deg.)90.00, 102.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GTP-binding protein / Arf GTPase


Mass: 21610.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Arf GTPase / Source: (gene. exp.) Asgard group archaeon (archaea) / Gene: FK733_07565 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8J7ZFD1
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.12 Å3/Da / Density % sol: 42.07 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 8000, 0.2 M Calcium acetate, 0.1M Sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980097 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980097 Å / Relative weight: 1
ReflectionResolution: 1.65→45.73 Å / Num. obs: 39833 / % possible obs: 91.8 % / Redundancy: 5.4 % / CC1/2: 0.999 / Rrim(I) all: 0.07 / Net I/σ(I): 14.8
Reflection shellResolution: 1.65→1.71 Å / Num. unique obs: 2142 / CC1/2: 0.734 / Rrim(I) all: 0.73

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (20-OCT-2021)refinement
ARP/wARPmodel building
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.653→45.73 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.929 / SU R Cruickshank DPI: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.129 / SU Rfree Blow DPI: 0.118 / SU Rfree Cruickshank DPI: 0.115
RfactorNum. reflection% reflectionSelection details
Rfree0.2402 1974 4.96 %RANDOM
Rwork0.2122 ---
obs0.2136 39833 91.7 %-
Displacement parametersBiso mean: 24.64 Å2
Baniso -1Baniso -2Baniso -3
1-2.1394 Å20 Å20.3508 Å2
2---3.5415 Å20 Å2
3---1.4021 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.653→45.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2813 0 58 314 3185
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082933HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.973982HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1053SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes513HARMONIC5
X-RAY DIFFRACTIONt_it2933HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.18
X-RAY DIFFRACTIONt_other_torsion15.75
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion389SEMIHARMONIC5
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_contact2741SEMIHARMONIC4
LS refinement shellResolution: 1.653→1.66 Å
RfactorNum. reflection% reflection
Rfree0.2898 -6.02 %
Rwork0.2638 749 -
obs--95.35 %
Refinement TLS params.Method: refined / Origin x: 24.3554 Å / Origin y: 17.4896 Å / Origin z: 51.7624 Å
111213212223313233
T0.0875 Å2-0.0072 Å20.0288 Å2-0.0595 Å20.0132 Å2--0.0492 Å2
L0.0949 °2-0.0803 °20.001 °2-0.3018 °20.3483 °2--0.5591 °2
S-0.0099 Å °0.0131 Å °-0.003 Å °0.0029 Å °0.0108 Å °0.0212 Å °0.0458 Å °0.021 Å °-0.0009 Å °
Refinement TLS groupSelection details: { *|* }

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