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- PDB-5mko: [2Fe-2S] cluster containing TtuA in complex with AMP. -

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Basic information

Entry
Database: PDB / ID: 5mko
Title[2Fe-2S] cluster containing TtuA in complex with AMP.
ComponentsTtuA PH0300
KeywordsRNA / TtuA / PH0300 / AMP / 2Fe-2S / Thiolation / tRNA modification enzyme / [Fe-S] cluster / iron-sulfur cluster
Function / homology
Function and homology information


Transferases; Transferring sulfur-containing groups; Sulfurtransferases / tRNA thio-modification / tRNA wobble uridine modification / 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
ADENOSINE MONOPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / tRNA-5-methyluridine(54) 2-sulfurtransferase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsArragain, S. / Bimai, O. / Legrand, P. / Golinelli-Pimpaneau, B.
Funding support France, 2items
OrganizationGrant numberCountry
LABEX DYNAMOLABEX 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 / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
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 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: TtuA PH0300
B: TtuA PH0300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,15310
Polymers71,8462
Non-polymers1,3088
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-47 kcal/mol
Surface area30670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.860, 72.320, 128.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TtuA PH0300


Mass: 35922.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Gene: PH0300 / Plasmid: pBG102 / Details (production host): codon optimised / Production host: Escherichia coli (E. coli) / References: UniProt: O58038
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe2S2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.23 Å3/Da / Density % sol: 44.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 8% PEG 3350, 2.5% DMF, NaCl 0.2M

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: 80
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 17292 / % possible obs: 99.8 % / Redundancy: 12.1 % / Biso Wilson estimate: 92.46 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.096 / Net I/σ(I): 13.2
Reflection shellResolution: 2.65→2.72 Å / Redundancy: 12.7 % / Rmerge(I) obs: 4.76 / Mean I/σ(I) obs: 0.9 / CC1/2: 0.463 / % 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: 2.65→45 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.93 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.349
RfactorNum. reflection% reflectionSelection details
Rfree0.239 878 5.08 %RANDOM
Rwork0.211 ---
obs0.213 17292 89.9 %-
Displacement parametersBiso mean: 88.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.2455 Å20 Å20 Å2
2--7.2049 Å20 Å2
3----7.4504 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: 1 / Resolution: 2.65→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4927 0 58 57 5042
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085089HARMONIC2
X-RAY DIFFRACTIONt_angle_deg16831HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1852SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes107HARMONIC2
X-RAY DIFFRACTIONt_gen_planes744HARMONIC5
X-RAY DIFFRACTIONt_it5089HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.33
X-RAY DIFFRACTIONt_other_torsion18.55
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion644SEMIHARMONIC5
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_contact5671SEMIHARMONIC4
LS refinement shellResolution: 2.65→2.81 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.282 -5.74 %
Rwork0.249 1413 -
all0.251 1499 -
obs--49.18 %
Refinement TLS params.Method: refined / Origin x: -4.3493 Å / Origin y: 22.6674 Å / Origin z: 15.9846 Å
111213212223313233
T-0.0691 Å20.0433 Å2-0.0377 Å2-0.0862 Å2-0.0339 Å2---0.0925 Å2
L0.7245 °20.2437 °2-0.233 °2-0.9436 °2-0.3236 °2--1.8825 °2
S-0.04 Å °0.0589 Å °0.0896 Å °0.0177 Å °-0.0027 Å °0.1024 Å °-0.1957 Å °-0.0897 Å °0.0427 Å °
Refinement TLS groupSelection details: { *|* }

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