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- PDB-6xp8: The crystal structure of TfuA involved in peptide backbone thioam... -

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Basic information

Entry
Database: PDB / ID: 6xp8
TitleThe crystal structure of TfuA involved in peptide backbone thioamidation from Methanosarcina acetivorans
ComponentsTfuA domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / YcaO / TfuA / thioamidation
Function / homologyTfuA-like, core / TfuA-like protein / TfuA-like core domain-containing protein
Function and homology information
Biological speciesMethanosarcina acetivorans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsDong, S.-H. / Nair, S.K.
CitationJournal: Nat.Chem.Biol. / Year: 2021
Title: Functional elucidation of TfuA in peptide backbone thioamidation.
Authors: Liu, A. / Si, Y. / Dong, S.H. / Mahanta, N. / Penkala, H.N. / Nair, S.K. / Mitchell, D.A.
History
DepositionJul 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TfuA domain-containing protein


Theoretical massNumber of molelcules
Total (without water)23,8871
Polymers23,8871
Non-polymers00
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.475, 36.837, 59.959
Angle α, β, γ (deg.)90.000, 121.770, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-501-

HOH

21A-533-

HOH

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Components

#1: Protein TfuA domain-containing protein


Mass: 23887.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TUA9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.03 Å3/Da / Density % sol: 39.51 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium citrate tribasic/citric acid pH 5.5 and 40% (v/v) PEG 600

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.65→25 Å / Num. obs: 23292 / % possible obs: 99.8 % / Redundancy: 7.4 % / CC1/2: 0.999 / Net I/σ(I): 21.4
Reflection shellResolution: 1.65→10 Å / Num. unique obs: 22138 / CC1/2: 0.787

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→25 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.557 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2339 1144 4.9 %RANDOM
Rwork0.1959 ---
obs0.1978 22138 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 50.65 Å2 / Biso mean: 22.01 Å2 / Biso min: 12.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å2-0 Å2-0.73 Å2
2---0.2 Å2-0 Å2
3---0.34 Å2
Refinement stepCycle: final / Resolution: 1.65→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1681 0 0 238 1919
Biso mean---31.42 -
Num. residues----217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191707
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.9772305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.075216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.55824.53375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07315310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3541511
X-RAY DIFFRACTIONr_chiral_restr0.0850.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211266
LS refinement shellResolution: 1.652→1.695 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.256 84 -
Rwork0.2 1606 -
obs--99.59 %

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