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- PDB-7f8m: Roadblock from Thorarchaeota SMTZ1-45 -

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Basic information

Entry
Database: PDB / ID: 7f8m
TitleRoadblock from Thorarchaeota SMTZ1-45
ComponentsRobl_LC7 domain-containing protein
KeywordsUNKNOWN FUNCTION / Asgard archaea / MGLB / roadblock
Function / homology: / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Roadblock/LAMTOR2 domain-containing protein
Function and homology information
Biological speciesCandidatus Thorarchaeota archaeon SMTZ1-45 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.14 Å
AuthorsRobinson, R.C. / Tran, L.T.
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 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
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.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Robl_LC7 domain-containing protein
B: Robl_LC7 domain-containing protein
C: Robl_LC7 domain-containing protein
D: Robl_LC7 domain-containing protein
E: Robl_LC7 domain-containing protein
F: Robl_LC7 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)76,5036
Polymers76,5036
Non-polymers00
Water5,513306
1
A: Robl_LC7 domain-containing protein
D: Robl_LC7 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)25,5012
Polymers25,5012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-15 kcal/mol
Surface area11460 Å2
MethodPISA
2
B: Robl_LC7 domain-containing protein
C: Robl_LC7 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)25,5012
Polymers25,5012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-12 kcal/mol
Surface area11820 Å2
MethodPISA
3
E: Robl_LC7 domain-containing protein
F: Robl_LC7 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)25,5012
Polymers25,5012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-14 kcal/mol
Surface area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.982, 58.982, 193.952
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

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Components

#1: Protein
Robl_LC7 domain-containing protein


Mass: 12750.568 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Thorarchaeota archaeon SMTZ1-45 (archaea)
Gene: AM325_09185 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A135VIJ8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 100 mM CH3COONa pH 5.0, 200 mM LiCl 16% PEG 6000

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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: Mar 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→20 Å / Num. obs: 40561 / % possible obs: 99 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.043 / Rsym value: 0.095 / Net I/σ(I): 35.2
Reflection shellResolution: 2.14→2.19 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3449 / CC1/2: 0.664 / Rpim(I) all: 0.332 / Rrim(I) all: 0.689 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.14→20 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.26 1993 -
Rwork0.191 --
obs-40550 97.6 %
Displacement parametersBiso mean: 37.96 Å2
Refinement stepCycle: LAST / Resolution: 2.14→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5238 0 0 306 5544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.025338
X-RAY DIFFRACTIONf_angle_d2.24287242
X-RAY DIFFRACTIONf_chiral_restr0.1019914
X-RAY DIFFRACTIONf_plane_restr0.0117931
X-RAY DIFFRACTIONf_dihedral_angle_d22.78911988
LS refinement shellResolution: 2.14→2.22 Å
RfactorNum. reflection% reflection
Rfree0.308 148 -
Rwork0.265 3453 -
obs--82.6 %

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