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- PDB-6ia6: Crystal structure of the bacterial Dehalococcoides mccartyi Elp3 ... -

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Basic information

Entry
Database: PDB / ID: 6ia6
TitleCrystal structure of the bacterial Dehalococcoides mccartyi Elp3 with desulfo-CoA
ComponentsELP3 family, ELP3 family
KeywordsTRANSFERASE / tRNA binding / Elongator complex / non-canonical acetyltransferase / acetyl-CoA hydrolysis
Function / homology
Function and homology information


tRNA uridine(34) acetyltransferase activity / tRNA carboxymethyluridine synthase / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / tRNA acetylation / tRNA wobble uridine modification / S-adenosyl-L-methionine binding / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / tRNA binding / metal ion binding / cytoplasm
Similarity search - Function
Radical SAM, C-terminal extension / Elongator complex protein 3-like / ELP3/YhcC / Radical_SAM C-terminal domain / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Acetyltransferase (GNAT) family ...Radical SAM, C-terminal extension / Elongator complex protein 3-like / ELP3/YhcC / Radical_SAM C-terminal domain / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Acetyltransferase (GNAT) family / Acyl-CoA N-acyltransferase / Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
DESULFO-COENZYME A / FE2/S2 (INORGANIC) CLUSTER / PHOSPHATE ION / tRNA uridine(34) acetyltransferase
Similarity search - Component
Biological speciesDehalococcoides mccartyi BTF08 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLin, T.Y. / Glatt, S.
Funding support Poland, 2items
OrganizationGrant numberCountry
Homing/2016-2/14 Poland
UMO-2015/19/B/NZ1/00343 Poland
CitationJournal: Nat Commun / Year: 2019
Title: The Elongator subunit Elp3 is a non-canonical tRNA acetyltransferase.
Authors: Lin, T.Y. / Abbassi, N.E.H. / Zakrzewski, K. / Chramiec-Glabik, A. / Jemiola-Rzeminska, M. / Rozycki, J. / Glatt, S.
History
DepositionNov 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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

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Assembly

Deposited unit
A: ELP3 family, ELP3 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9474
Polymers49,9411
Non-polymers1,0063
Water00
1
A: ELP3 family, ELP3 family
hetero molecules

A: ELP3 family, ELP3 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,8948
Polymers99,8822
Non-polymers2,0136
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5310 Å2
ΔGint-62 kcal/mol
Surface area31700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.540, 160.740, 92.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-502-

FES

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Components

#1: Protein ELP3 family, ELP3 family


Mass: 49940.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Dehalococcoides mccartyi Elp3 and desulfo-CoA
Source: (gene. exp.) Dehalococcoides mccartyi BTF08 (bacteria)
Gene: btf_573
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1C7D1B7
#2: Chemical ChemComp-DCA / DESULFO-COENZYME A


Mass: 735.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4

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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: 2.7 Å3/Da / Density % sol: 54.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 100 mM MES, pH 6.3 and 4% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 15372 / % possible obs: 99 % / Redundancy: 4.4 % / Rrim(I) all: 0.141 / Net I/σ(I): 9.75
Reflection shellResolution: 2.7→2.77 Å / Rrim(I) all: 2.099

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L7L

5l7l


Resolution: 2.7→43.305 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.48
RfactorNum. reflection% reflectionSelection details
Rfree0.2685 772 5.02 %random selection
Rwork0.2232 ---
obs0.2254 15372 98.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→43.305 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3073 0 0 0 3073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023138
X-RAY DIFFRACTIONf_angle_d0.4914253
X-RAY DIFFRACTIONf_dihedral_angle_d14.371876
X-RAY DIFFRACTIONf_chiral_restr0.039470
X-RAY DIFFRACTIONf_plane_restr0.003537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6998-2.86890.37681260.38012386X-RAY DIFFRACTION99
2.8689-3.09030.34721260.33142397X-RAY DIFFRACTION99
3.0903-3.40120.30981280.27962423X-RAY DIFFRACTION99
3.4012-3.89310.30231280.2312415X-RAY DIFFRACTION99
3.8931-4.90380.23551300.18932460X-RAY DIFFRACTION99
4.9038-43.31060.23881340.1922519X-RAY DIFFRACTION98

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