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- PDB-8oum: Arf GTPase from the asgard Gerdarchaea : GerdArfR1 bound to GTP -

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Basic information

Entry
Database: PDB / ID: 8oum
TitleArf GTPase from the asgard Gerdarchaea : GerdArfR1 bound to GTP
ComponentsGTP-binding proteinG protein
KeywordsSIGNALING PROTEIN / GTPASE / GTP / ARF FAMILY / ASGARD ARCHAEA / Gerdarchaea
Function / homology
Function and homology information


GTPase activity / GTP binding
Similarity search - Function
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'-TRIPHOSPHATE / GTP-binding protein
Similarity search - Component
Biological speciesAsgard group archaeon (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 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
C: GTP-binding protein
D: GTP-binding protein
E: GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,68915
Polymers100,9525
Non-polymers2,73710
Water2,198122
1
A: GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7383
Polymers20,1901
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7383
Polymers20,1901
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7383
Polymers20,1901
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7383
Polymers20,1901
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7383
Polymers20,1901
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.250, 54.880, 121.790
Angle α, β, γ (deg.)90.00, 94.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
GTP-binding protein / G protein / Arf GTPase


Mass: 20190.365 Da / Num. of mol.: 5
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-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 5 / 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.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.88 Å3/Da / Density % sol: 57.28 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 8.5% PEG 8000, 0.1M MgCl2 and 0.1M Tris pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980112 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980112 Å / Relative weight: 1
ReflectionResolution: 2.67→48 Å / Num. obs: 32436 / % possible obs: 97.8 % / Redundancy: 6.8 % / CC1/2: 0.99 / Rrim(I) all: 0.034 / Net I/σ(I): 6
Reflection shellResolution: 2.67→2.83 Å / Num. unique obs: 4627 / CC1/2: 0.446 / Rrim(I) all: 0.26

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (20-OCT-2021)refinement
XDSdata reduction
XSCALEdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→46.41 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.91 / SU R Cruickshank DPI: 0.7 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.69 / SU Rfree Blow DPI: 0.322 / SU Rfree Cruickshank DPI: 0.329
RfactorNum. reflection% reflectionSelection details
Rfree0.2673 1608 5 %RANDOM
Rwork0.236 ---
obs0.2376 32148 97 %-
Displacement parametersBiso mean: 68.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.6916 Å20 Å25.089 Å2
2---9.3792 Å20 Å2
3---6.6876 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 2.67→46.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6450 0 165 122 6737
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086731HARMONIC2
X-RAY DIFFRACTIONt_angle_deg19186HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2312SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1183HARMONIC5
X-RAY DIFFRACTIONt_it6731HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion19.86
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion921SEMIHARMONIC5
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_contact5136SEMIHARMONIC4
LS refinement shellResolution: 2.67→2.71 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.4356 -4.98 %
Rwork0.3828 611 -
all0.3857 643 -
obs--39.18 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.0803-0.53910.15311.94660.19598.236-0.0060.01930.13290.1232-0.1065-0.1016-0.2890.38470.1125-0.1762-0.0603-0.0912-0.08020.0181-0.253316.51540.04543.6418
24.5346-0.48261.31462.6241-0.25665.19510.12540.0828-0.02960.08750.0233-0.01920.1020.1854-0.1486-0.21210.0164-0.06530.1184-0.0133-0.26997.9203-2.0702-24.9671
39.1692-2.11691.98892.71230.04598.09560.1372-0.1405-0.2984-0.1380.06430.09460.082-0.2908-0.2015-0.3187-0.0316-0.08740.0990.0278-0.303332.9022-15.4303-48.0008
44.5502-0.20081.03863.526-1.4794.97460.01-0.25480.05570.12750.11690.11950.1593-0.2176-0.1269-0.26440.055-0.04490.0905-0.0111-0.241955.3068-18.5545-28.1574
56.543-1.5882.60742.1572-0.5536.85950.14230.4605-0.0187-0.0023-0.07270.2009-0.10180.4645-0.0695-0.20250.0032-0.07560.0848-0.0446-0.1987-3.65534.7416-51.299
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }

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