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- PDB-5l7j: Crystal Structure of Elp3 from Dehalococcoides mccartyi -

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Basic information

Entry
Database: PDB / ID: 5l7j
TitleCrystal Structure of Elp3 from Dehalococcoides mccartyi
ComponentsELP3 family
KeywordsTRANSLATION / Elongator / tRNA modification / Elp3
Function / homology
Function and homology information


tRNA carboxymethyluridine synthase / acyltransferase activity / 2 iron, 2 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 / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / tRNA carboxymethyluridine synthase / :
Similarity search - Component
Biological speciesDehalococcoides mccartyi BTF08 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 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 2.0Nov 13, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ELP3 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0143
Polymers51,7731
Non-polymers2412
Water68538
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-46 kcal/mol
Surface area17340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.460, 158.580, 93.580
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

31A-626-

HOH

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Components

#1: Protein ELP3 family


Mass: 51772.934 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: A0A1C7D1B6*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


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.73 Å3/Da / Density % sol: 54.96 %
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: 0.97923 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 58785 / % possible obs: 99.5 % / Redundancy: 10.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Net I/σ(I): 14.2
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 10.6 % / Rmerge(I) obs: 2.309 / Mean I/σ(I) obs: 1.03 / CC1/2: 0.567 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→43.294 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.56
RfactorNum. reflection% reflection
Rfree0.219 2936 5 %
Rwork0.1911 --
obs0.1925 58703 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.15→43.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3165 0 5 38 3208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023252
X-RAY DIFFRACTIONf_angle_d0.6214389
X-RAY DIFFRACTIONf_dihedral_angle_d10.8721227
X-RAY DIFFRACTIONf_chiral_restr0.023488
X-RAY DIFFRACTIONf_plane_restr0.003561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.18530.38631342578X-RAY DIFFRACTION97
2.1853-2.2230.36761382651X-RAY DIFFRACTION99
2.223-2.26340.34781372636X-RAY DIFFRACTION99
2.2634-2.30690.33921372653X-RAY DIFFRACTION99
2.3069-2.3540.26241422640X-RAY DIFFRACTION99
2.354-2.40520.38261412645X-RAY DIFFRACTION99
2.4052-2.46110.28961422663X-RAY DIFFRACTION100
2.4611-2.52270.28161362668X-RAY DIFFRACTION100
2.5227-2.59090.25631402649X-RAY DIFFRACTION100
2.5909-2.66710.31921432657X-RAY DIFFRACTION100
2.6671-2.75320.2741362651X-RAY DIFFRACTION99
2.7532-2.85160.26771422680X-RAY DIFFRACTION100
2.8516-2.96570.26261432636X-RAY DIFFRACTION100
2.9657-3.10060.2771402683X-RAY DIFFRACTION100
3.1006-3.26410.2281352671X-RAY DIFFRACTION100
3.2641-3.46850.17571412682X-RAY DIFFRACTION100
3.4685-3.73620.23031360.17512646X-RAY DIFFRACTION100
3.7362-4.11190.18081450.16412655X-RAY DIFFRACTION100
4.1119-4.70630.19171410.13852671X-RAY DIFFRACTION100
4.7063-5.9270.17941450.15432675X-RAY DIFFRACTION100
5.927-43.2940.18811420.16542677X-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)
13.9404-1.31920.83637.58-2.88912.34530.2690.32960.1358-0.58980.1140.6106-0.018-0.1039-0.33720.6195-0.0533-0.02340.51430.03870.4413-36.5722-17.87967.8599
23.30030.0319-1.12413.0338-0.95414.61230.14490.14750.3743-0.2342-0.0196-0.176-0.2290.1377-0.09410.4312-0.0120.01580.3757-0.03580.3873-25.2832-20.92276.6252
37.0104-3.0291-1.08814.34280.86864.49030.48341.2467-0.0475-0.8338-0.48340.471-0.3562-0.627-0.02120.8220.0237-0.04050.82270.04720.4663-32.0811-18.6765-11.2415
42.9629-0.5956-0.75914.3149-0.6496.330.0863-0.2119-0.0583-0.2604-0.1742-0.64520.46730.7840.08540.50310.14250.07440.76580.02130.604-9.1402-33.25642.7362
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 218 )
3X-RAY DIFFRACTION3chain 'A' and (resid 219 through 277 )
4X-RAY DIFFRACTION4chain 'A' and (resid 278 through 459 )

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