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- PDB-7f8f: Roadblock from Odinarchaeota LCB_4 -

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Basic information

Entry
Database: PDB / ID: 7f8f
TitleRoadblock from Odinarchaeota LCB_4
ComponentsRobl_LC7 domain-containing protein
KeywordsUNKNOWN FUNCTION / Asgard archaea / MGLB / roadblock
Function / homologyRoadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Robl_LC7 domain-containing protein
Function and homology information
Biological speciesCandidatus Odinarchaeota archaeon LCB_4 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsRobinson, R.C. / Akil, C.
Funding support Japan, United States, 3items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR19S5 Japan
Japan Society for the Promotion of Science (JSPS)JP20H00476 Japan
Other privateMoore and Simons foundations GBMF9743 United States
CitationJournal: Commun Biol / Year: 2024
Title: The eukaryotic-like characteristics of small GTPase, roadblock and TRAPPC3 proteins from Asgard archaea
Authors: Tran, L.T. / Akil, C. / Senju, Y. / Robinson, R.C.
History
DepositionJul 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 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
Revision 1.2Jan 29, 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.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Robl_LC7 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)10,4381
Polymers10,4381
Non-polymers00
Water81145
1
A: Robl_LC7 domain-containing protein

A: Robl_LC7 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)20,8762
Polymers20,8762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Buried area3010 Å2
ΔGint-18 kcal/mol
Surface area8700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.072, 59.245, 59.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Space group name HallI2b2c
Symmetry operation#1: x,y,z
#2: x,-y,-z+1/2
#3: -x+1/2,y,-z
#4: -x,-y+1/2,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1
#7: -x+1,y+1/2,-z+1/2
#8: -x+1/2,-y+1,z+1/2
Components on special symmetry positions
IDModelComponents
11A-143-

HOH

21A-144-

HOH

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Components

#1: Protein Robl_LC7 domain-containing protein


Mass: 10438.052 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Odinarchaeota archaeon LCB_4 (archaea)
Strain: LCB_4 / Gene: OdinLCB4_13320 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q9N7N8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 200 mM MgSO4 20% PEG 4000 10% glycerol

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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: Oct 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→42.1 Å / Num. obs: 8418 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.019 / Rrim(I) all: 0.05 / Net I/σ(I): 18.5
Reflection shellResolution: 1.83→1.87 Å / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 813 / CC1/2: 0.889 / Rpim(I) all: 0.211 / Rrim(I) all: 0.566

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Processing

Software
NameVersionClassification
PHENIXv1.17.1refinement
HKL-2000data reduction
HKL-2000data scaling
ACORNphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3l7h

3l7h


Resolution: 1.83→39.3 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.216 813 -
Rwork0.193 --
obs-8417 99.9 %
Displacement parametersBiso mean: 32.34 Å2
Refinement stepCycle: LAST / Resolution: 1.83→39.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms621 0 0 45 666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0019647
X-RAY DIFFRACTIONf_angle_d0.4482879
X-RAY DIFFRACTIONf_chiral_restr0.0427113
X-RAY DIFFRACTIONf_plane_restr0.0016110
X-RAY DIFFRACTIONf_dihedral_angle_d24.2335254
LS refinement shellResolution: 1.83→2.1 Å
RfactorNum. reflection% reflection
Rfree0.22 40 -
Rwork0.201 403 -
obs--99.6 %

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