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- PDB-6scy: U34-tRNA thiolase NcsA from Methanococcus maripaludis with its [4... -

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Basic information

Entry
Database: PDB / ID: 6scy
TitleU34-tRNA thiolase NcsA from Methanococcus maripaludis with its [4Fe-4S] cluster
Components([4Fe-4S]-dependent U34-ARNt ...) x 2
KeywordsRNA BINDING PROTEIN / tRNA thiolase / iron-sulfur cluster
Function / homology
Function and homology information


tRNA thio-modification / tRNA wobble uridine modification / transferase activity / 4 iron, 4 sulfur cluster binding / tRNA binding / ATP binding / metal ion binding
Similarity search - Function
Cytoplasmic tRNA 2-thiolation protein 1 / tRNA thiolation protein, TtcA/Ctu1 type / : / 2-thiouridine synthetase TtuA, N-terminal LIM domain / tRNA(Ile)-lysidine/2-thiocytidine synthase, N-terminal / PP-loop domain / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Uncharacterized protein
Similarity search - Component
Biological speciesMethanococcus maripaludis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsBimai, O. / Legrand, P. / Golinelli-Pimpaneau, B.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-11-LABX-0011 France
CitationJournal: Sci Rep / Year: 2023
Title: The thiolation of uridine 34 in tRNA, which controls protein translation, depends on a [4Fe-4S] cluster in the archaeum Methanococcus maripaludis.
Authors: Bimai, O. / Legrand, P. / Ravanat, J.L. / Touati, N. / Zhou, J. / He, N. / Lenon, M. / Barras, F. / Fontecave, M. / Golinelli-Pimpaneau, B.
History
DepositionJul 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation / citation_author / database_2
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.3Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: [4Fe-4S]-dependent U34-ARNt thiolase
B: [4Fe-4S]-dependent U34-ARNt thiolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,79153
Polymers70,5042
Non-polymers5,28851
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11130 Å2
ΔGint-685 kcal/mol
Surface area33300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.980, 84.480, 145.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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[4Fe-4S]-dependent U34-ARNt ... , 2 types, 2 molecules AB

#1: Protein [4Fe-4S]-dependent U34-ARNt thiolase


Mass: 35127.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis (strain S2 / LL) (archaea)
Gene: MMP1356 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6LXJ4
#2: Protein [4Fe-4S]-dependent U34-ARNt thiolase


Mass: 35376.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis (strain S2 / LL) (archaea)
Gene: MMP1356 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6LXJ4

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Non-polymers , 4 types, 230 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 45 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: anaerobic conditions (glove box). 0.1M HEPES pH 7.5, 0.2 M ammonium sulfate, 18% (w/v) PEG 4000, 10% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980096 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 7, 2016 / Details: KB mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980096 Å / Relative weight: 1
ReflectionResolution: 2.79→48.48 Å / Num. obs: 17385 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 94.14 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.088 / Rrim(I) all: 0.194 / Rsym value: 0.183 / Χ2: 1.04 / Net I/av σ(I): 7.5 / Net I/σ(I): 7.5
Reflection shellResolution: 2.79→2.86 Å / Redundancy: 9 % / Rmerge(I) obs: 6.89 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 1150 / CC1/2: 0.146 / Rpim(I) all: 2.366 / Rrim(I) all: 7.304 / Rsym value: 6.89 / Χ2: 0.69 / % possible all: 91.5

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDS20170615data reduction
XDS20170615data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VRH

3vrh


Resolution: 2.81→31.85 Å / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.561
RfactorNum. reflection% reflectionSelection details
Rfree0.287 645 4.89 %random
Rwork0.209 ---
obs0.213 13180 76.7 %-
Displacement parametersBiso mean: 99.04 Å2
Baniso -1Baniso -2Baniso -3
1-3.006 Å20 Å20 Å2
2--1.1605 Å20 Å2
3----4.1666 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 2.81→31.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4733 0 245 179 5157
LS refinement shellResolution: 2.81→2.97 Å
RfactorNum. reflection% reflection
Rfree0.2165 17 4.13 %
Rwork0.2238 395 -
obs--15.68 %

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