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- PDB-5mkp: Non redox thiolation in transfer RNAs occuring via sulfur activat... -

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Basic information

Entry
Database: PDB / ID: 5mkp
TitleNon redox thiolation in transfer RNAs occuring via sulfur activation by a [4Fe-4S] cluster
ComponentsPH0300
KeywordsRNA / TtuA / [4Fe-5S] / sulfur insertion / tRNA modification / thiolation reaction / iron-sulfur cluster
Function / homology
Function and homology information


Transferases; Transferring sulfur-containing groups; Sulfurtransferases / cytosolic tRNA wobble base thiouridylase complex / tRNA wobble position uridine thiolation / 4 iron, 4 sulfur cluster binding / transferase activity / tRNA binding / ATP binding / metal ion binding
Similarity search - Function
Cytoplasmic tRNA 2-thiolation protein 1 / tRNA thiolation protein, TtcA/Ctu1 type / tRNA(Ile)-lysidine/2-thiocytidine synthase, N-terminal / PP-loop family / Rhodanese-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Fe4 H S5 / tRNA-5-methyluridine(54) 2-sulfurtransferase
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsArragain, S. / Bimai, O. / Legrand, P. / Golinelli-Pimpaneau, B.
Funding support France, 2items
OrganizationGrant numberCountry
LABEXLABEX DYNAMO France
French National Research AgencyANR-11-LABX-0011 France
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Nonredox thiolation in tRNA occurring via sulfur activation by a [4Fe-4S] cluster.
Authors: Arragain, S. / Bimai, O. / Legrand, P. / Caillat, S. / Ravanat, J.L. / Touati, N. / Binet, L. / Atta, M. / Fontecave, M. / Golinelli-Pimpaneau, B.
History
DepositionDec 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Structure summary / Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _entity.pdbx_description
Revision 1.2Jul 12, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jul 19, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 31, 2018Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.6Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PH0300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4384
Polymers35,9231
Non-polymers5163
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.120, 70.120, 127.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PH0300


Mass: 35922.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Gene: PH0300 / Plasmid: pBG102-TtuA-PH0300 / Details (production host): clivable tag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O58038
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-Q46 / Fe4 H S5


Mass: 384.713 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4HS5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.77 % / Description: Diamond
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: Anaerobic conditions (Glovebox)

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: PX2
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.979338 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionBiso Wilson estimate: 79.78 Å2
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 13.9 % / Rmerge(I) obs: 2.77 / Mean I/σ(I) obs: 1 / CC1/2: 0.29 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VRH

3vrh


Resolution: 2.5→47.25 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.931 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.702 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.193 / SU Rfree Blow DPI: 0.294 / SU Rfree Cruickshank DPI: 0.288
RfactorNum. reflection% reflectionSelection details
Rfree0.245 582 5.01 %RANDOM
Rwork0.193 ---
obs0.195 11624 100 %-
Displacement parametersBiso mean: 78.52 Å2
Baniso -1Baniso -2Baniso -3
1--6.8416 Å20 Å20 Å2
2---6.8416 Å20 Å2
3---13.6832 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: 1 / Resolution: 2.5→47.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2471 0 11 92 2574
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092570HARMONIC2
X-RAY DIFFRACTIONt_angle_deg13461HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d927SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes54HARMONIC2
X-RAY DIFFRACTIONt_gen_planes369HARMONIC5
X-RAY DIFFRACTIONt_it2570HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion18.44
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion322SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance4HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2931SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.74 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.275 135 5.01 %
Rwork0.229 2558 -
all0.232 2693 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -16.5569 Å / Origin y: 10.5856 Å / Origin z: 10.0633 Å
111213212223313233
T-0.1501 Å20.0207 Å20.0396 Å2--0.0311 Å2-0.0185 Å2---0.1013 Å2
L0.9945 °20.4932 °20.3828 °2-1.493 °20.109 °2--2.0734 °2
S-0.019 Å °0.01 Å °-0.0208 Å °0.0598 Å °0.0503 Å °-0.0275 Å °0.0621 Å °0.2103 Å °-0.0313 Å °
Refinement TLS groupSelection details: { *|* }

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