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- PDB-6ia8: Apo crystal structure of archaeal Methanocaldococcus infernus Elp... -

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Basic information

Entry
Database: PDB / ID: 6ia8
TitleApo crystal structure of archaeal Methanocaldococcus infernus Elp3 (del1-19)
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
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 / 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: 1.9 Å
AuthorsLin, T.Y. / Glatt, S.
Funding support Poland, 2items
OrganizationGrant numberCountry
Homing/2016-2/14 Poland
Polish National Science CentreUMO-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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone acetyltransferase, ELP3 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5498
Polymers59,8761
Non-polymers6727
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-103 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.440, 63.440, 250.220
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: 59876.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: apo structure of Methanocaldococcus infernus Elp3 (del1-19)
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.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.1 Å3/Da / Density % sol: 41.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M phosphate/citrate (pH 3.8), 0.2 M LiSO4 and 12% PEG1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 41022 / % possible obs: 98.3 % / Redundancy: 24.1 % / Rrim(I) all: 0.068 / Net I/σ(I): 33.38
Reflection shellResolution: 1.9→1.95 Å / Rrim(I) all: 1.582

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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: 1.9→44.859 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.58
RfactorNum. reflection% reflectionSelection details
Rfree0.2147 2052 5 %random selection
Rwork0.1799 ---
obs0.1816 41022 98.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→44.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3467 0 35 120 3622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093585
X-RAY DIFFRACTIONf_angle_d0.844817
X-RAY DIFFRACTIONf_dihedral_angle_d17.7842201
X-RAY DIFFRACTIONf_chiral_restr0.057513
X-RAY DIFFRACTIONf_plane_restr0.006605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8972-1.94140.43271130.36712152X-RAY DIFFRACTION83
1.9414-1.98990.25721260.27022386X-RAY DIFFRACTION92
1.9899-2.04370.29291350.22112565X-RAY DIFFRACTION99
2.0437-2.10390.25081350.20142553X-RAY DIFFRACTION100
2.1039-2.17180.24091360.18392603X-RAY DIFFRACTION100
2.1718-2.24940.24571380.18122608X-RAY DIFFRACTION100
2.2494-2.33940.2231370.18172608X-RAY DIFFRACTION100
2.3394-2.44590.21041380.17912623X-RAY DIFFRACTION100
2.4459-2.57490.21871370.18272601X-RAY DIFFRACTION100
2.5749-2.73620.22491390.18862636X-RAY DIFFRACTION100
2.7362-2.94740.221380.19212632X-RAY DIFFRACTION100
2.9474-3.24390.23791410.1912664X-RAY DIFFRACTION100
3.2439-3.71310.18911410.17062696X-RAY DIFFRACTION100
3.7131-4.67730.1711440.13792722X-RAY DIFFRACTION100
4.6773-44.87140.22611540.19012921X-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)
15.55351.92890.29422.7083-0.09432.57730.0783-0.23550.02260.2462-0.12370.09920.0579-0.16440.04680.35660.00210.02750.2740.04560.2683-27.8848-7.9288-11.3838
21.4918-0.4794-0.84182.25591.70633.46050.0151-0.22160.09890.2559-0.16250.11570.023-0.22610.17750.2247-0.0473-0.00810.324-0.00760.2437-19.640416.0076-9.3319
32.48222.1343.6824.6025.08436.7691-0.1011-0.08710.15640.09260.12220.08770.10180.11610.07150.21220.0350.00490.29330.04580.2567-32.223818.91-26.7206
42.0104-0.4160.12552.1141-0.49231.62310.0060.1563-0.2857-0.1693-0.01440.11470.2149-0.1579-0.01150.2225-0.00940.01870.2505-0.02230.2606-19.8244-0.8133-32.4323
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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