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- PDB-6iaz: The archaeal Methanocaldococcus infernus Elp3 with N-terminus del... -

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Basic information

Entry
Database: PDB / ID: 6iaz
TitleThe archaeal Methanocaldococcus infernus Elp3 with N-terminus deletion (1-46)
ComponentsHistone acetyltransferase, 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 / 4 iron, 4 sulfur cluster binding / tRNA binding / metal ion binding / cytoplasm
Similarity search - Function
: / ELP3 N-terminal domain / 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. ...: / ELP3 N-terminal domain / 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 / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aldolase-type TIM barrel
Similarity search - Domain/homology
tRNA uridine(34) acetyltransferase
Similarity search - Component
Biological speciesMethanocaldococcus infernus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsLin, T.Y. / Glatt, S.
Funding support Poland, 3items
OrganizationGrant numberCountry
Homing/2016-2/14 Poland
Polish National Science CentreUMO-2015/19/B/NZ1/00343 Poland
TEAM TECH CORE FACILITY/2017-4/6 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 28, 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone acetyltransferase, ELP3 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3677
Polymers56,7901
Non-polymers5766
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-91 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.350, 63.350, 250.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Histone acetyltransferase, ELP3 family


Mass: 56790.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The archaeal Methanocaldococcus infernus Elp3 with N-terminus deletion (1-46)
Source: (gene. exp.) Methanocaldococcus infernus (archaea) / Gene: Metin_0452
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: D5VRB9, histone acetyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1 M citrate (pH 3.8), 0.1 M LiCl and 17% PEG6000

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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 6M / Detector: PIXEL / Date: Aug 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 41281 / % possible obs: 99.8 % / Redundancy: 10.4 % / Rrim(I) all: 0.068 / Net I/σ(I): 19.34
Reflection shellResolution: 1.9→1.95 Å / Rrim(I) all: 0.997

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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: 1.901→34.818 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.82
RfactorNum. reflection% reflectionSelection details
Rfree0.2174 2064 5 %random selection
Rwork0.1947 ---
obs0.1958 41281 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.901→34.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3467 0 30 163 3660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073569
X-RAY DIFFRACTIONf_angle_d0.8254793
X-RAY DIFFRACTIONf_dihedral_angle_d16.5222192
X-RAY DIFFRACTIONf_chiral_restr0.051512
X-RAY DIFFRACTIONf_plane_restr0.005601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9011-1.94530.32921330.32462515X-RAY DIFFRACTION98
1.9453-1.99390.29081340.26582557X-RAY DIFFRACTION100
1.9939-2.04780.30981350.25142566X-RAY DIFFRACTION100
2.0478-2.10810.2661360.23422574X-RAY DIFFRACTION100
2.1081-2.17610.24781350.21072579X-RAY DIFFRACTION100
2.1761-2.25390.22111340.20762565X-RAY DIFFRACTION100
2.2539-2.34410.2421360.19272575X-RAY DIFFRACTION100
2.3441-2.45080.23621360.20442576X-RAY DIFFRACTION100
2.4508-2.57990.2491360.19752592X-RAY DIFFRACTION100
2.5799-2.74150.23541380.19952618X-RAY DIFFRACTION100
2.7415-2.95310.2211370.19732606X-RAY DIFFRACTION100
2.9531-3.25010.2141380.19442628X-RAY DIFFRACTION100
3.2501-3.71990.19551420.17582693X-RAY DIFFRACTION100
3.7199-4.68490.19011410.15612684X-RAY DIFFRACTION100
4.6849-34.82350.20191530.20962889X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.18962.06830.20652.9466-0.04323.14740.115-0.25250.03570.3795-0.16530.1590.1289-0.18930.06980.3418-0.01050.03420.24850.05620.2578-27.9467-8.0482-11.4697
21.7678-0.5705-0.38812.9271.70873.46430.0288-0.36730.15730.3367-0.19650.120.0205-0.25770.14030.2223-0.0595-0.00270.3525-0.00880.2629-19.594715.9786-9.3354
32.69553.39153.73778.56857.24576.6645-0.1318-0.08850.29820.04950.01370.1993-0.0757-0.06090.04340.19190.0268-0.01160.29360.04730.2787-32.099518.8821-26.6999
42.5378-0.728-0.19432.911-0.58181.59050.03490.1328-0.3182-0.1343-0.02750.20080.1803-0.09480.00720.2091-0.00560.01310.243-0.01220.2587-19.7557-0.815-32.4028
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 74 through 231 )
2X-RAY DIFFRACTION2chain 'A' and (resid 232 through 368 )
3X-RAY DIFFRACTION3chain 'A' and (resid 369 through 404 )
4X-RAY DIFFRACTION4chain 'A' and (resid 405 through 534 )

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