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- PDB-5l7l: Crystal Structure of Elp3 from Dehalococcoides mccartyi (390-407 ... -

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Basic information

Entry
Database: PDB / ID: 5l7l
TitleCrystal Structure of Elp3 from Dehalococcoides mccartyi (390-407 GSGSG)
ComponentsELP3 family, ELP3 family
KeywordsTRANSLATION / Elongator / tRNA modification / Elp3
Function / homology
Function and homology information


tRNA uridine(34) acetyltransferase activity / tRNA acetylation / tRNA wobble uridine modification / S-adenosyl-L-methionine binding / iron-sulfur cluster binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / 4 iron, 4 sulfur cluster binding / tRNA binding / metal ion binding
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 / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / tRNA uridine(34) acetyltransferase / :
Similarity search - Component
Biological speciesDehalococcoides mccartyi BTF08 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.593 Å
AuthorsGlatt, S. / Mueller, C.W.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Structural basis for tRNA modification by Elp3 from Dehalococcoides mccartyi.
Authors: Glatt, S. / Zabel, R. / Kolaj-Robin, O. / Onuma, O.F. / Baudin, F. / Graziadei, A. / Taverniti, V. / Lin, T.Y. / Baymann, F. / Seraphin, B. / Breunig, K.D. / Muller, C.W.
History
DepositionJun 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 21, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)49,8843
Polymers49,6421
Non-polymers2412
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-48 kcal/mol
Surface area17130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.760, 161.410, 93.220
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

21A-502-

FES

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Components

#1: Protein ELP3 family, ELP3 family


Mass: 49642.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dehalococcoides mccartyi BTF08 (bacteria)
Gene: btf_573 / Production host: Escherichia coli (E. coli) / References: UniProt: M1Q3U6, UniProt: A0A1C7D1B7*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2

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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: 2.79 Å3/Da / Density % sol: 55.99 %
Crystal growTemperature: 298 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
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 17592 / % possible obs: 99.6 % / Redundancy: 13.06 % / CC1/2: 0.999 / Rmerge(I) obs: 0.126 / Net I/σ(I): 14.8
Reflection shellResolution: 2.59→2.66 Å / Redundancy: 11.8 % / Rmerge(I) obs: 2.974 / Mean I/σ(I) obs: 0.94 / CC1/2: 0.364 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: trunctaed 5L7J

5l7j


Resolution: 2.593→46.61 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.46
RfactorNum. reflection% reflection
Rfree0.2187 880 5.01 %
Rwork0.1818 --
obs0.1836 17582 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.593→46.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3076 0 5 0 3081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043153
X-RAY DIFFRACTIONf_angle_d0.6844256
X-RAY DIFFRACTIONf_dihedral_angle_d10.6241183
X-RAY DIFFRACTIONf_chiral_restr0.025472
X-RAY DIFFRACTIONf_plane_restr0.003546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5934-2.75590.36671430.31412704X-RAY DIFFRACTION97
2.7559-2.96860.34451440.28912740X-RAY DIFFRACTION100
2.9686-3.26730.35171450.23162753X-RAY DIFFRACTION100
3.2673-3.73990.22891460.1782778X-RAY DIFFRACTION100
3.7399-4.71120.1761480.15552811X-RAY DIFFRACTION100
4.7112-46.61750.1871540.16562916X-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)
12.54730.4275-0.73816.9738-1.40113.27540.0737-0.14920.18170.21530.07820.0057-0.13850.0871-0.14650.5648-0.02240.01590.4744-0.03660.4319-29.3836-22.561713.0053
28.132-2.20740.7643.42790.03063.55650.36751.14610.3588-0.8565-0.3890.0178-0.4895-0.04740.02730.94950.03580.09720.67890.09170.6291-26.571-17.3878-8.4095
34.6272-1.174-1.32595.95620.97338.5153-0.0076-0.1841-0.1256-0.02850.1504-0.84030.15170.9108-0.11790.46910.07370.03060.73690.02860.7989-7.2876-32.90563.1115
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 151 )
2X-RAY DIFFRACTION2chain 'A' and (resid 152 through 313 )
3X-RAY DIFFRACTION3chain 'A' and (resid 314 through 446 )

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