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- PDB-5l4o: Structure of an E.coli initiator tRNAfMet A1-U72 variant -

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Basic information

Entry
Database: PDB / ID: 5l4o
TitleStructure of an E.coli initiator tRNAfMet A1-U72 variant
ComponentstRNA (76-MER)
KeywordsTRANSLATION / tRNA-Translation initiation
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.799 Å
AuthorsMonestier, A. / Schmitt, E. / Mechulam, Y.
Funding support France, 2items
OrganizationGrant numberCountry
CNRSUMR7654 France
Ecole polytechniqueUMR7654 France
CitationJournal: RNA / Year: 2017
Title: The structure of an E. coli tRNAf(Met) A1-U72 variant shows an unusual conformation of the A1-U72 base pair.
Authors: Monestier, A. / Aleksandrov, A. / Coureux, P.D. / Panvert, M. / Mechulam, Y. / Schmitt, E.
History
DepositionMay 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Atomic model / Structure summary
Revision 1.2Apr 26, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8572
Polymers24,8341
Non-polymers231
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-11 kcal/mol
Surface area12690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.150, 142.620, 202.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: RNA chain tRNA (76-MER)


Mass: 24833.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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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: 5.1 Å3/Da / Density % sol: 75.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 6000, 2M NaCl / PH range: 6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.79→41.23 Å / Num. obs: 13192 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.84 % / Biso Wilson estimate: 78.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 17.03
Reflection shellResolution: 2.79→2.95 Å / Redundancy: 9.74 % / Rmerge(I) obs: 2.464 / Mean I/σ(I) obs: 0.95 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CW5

3cw5


Resolution: 2.799→35.167 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.12
RfactorNum. reflection% reflection
Rfree0.2265 624 4.8 %
Rwork0.1969 --
obs0.1982 13004 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.799→35.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1623 1 5 1629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051812
X-RAY DIFFRACTIONf_angle_d1.142823
X-RAY DIFFRACTIONf_dihedral_angle_d15.405883
X-RAY DIFFRACTIONf_chiral_restr0.052375
X-RAY DIFFRACTIONf_plane_restr0.00776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7986-3.080.35891590.38413004X-RAY DIFFRACTION99
3.08-3.52540.24181440.22383052X-RAY DIFFRACTION98
3.5254-4.44020.24631690.19863070X-RAY DIFFRACTION100
4.4402-35.16940.19561520.16943254X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 7.1262 Å / Origin y: 17.3952 Å / Origin z: -17.5451 Å
111213212223313233
T0.9419 Å20.0798 Å20.0298 Å2-0.5869 Å20.0741 Å2--0.7827 Å2
L2.3437 °20.3424 °2-1.4025 °2-1.5002 °20.4743 °2--5.917 °2
S-0.0574 Å °0.4583 Å °-0.1723 Å °-0.2576 Å °-0.2462 Å °-0.0979 Å °0.6156 Å °0.404 Å °0.3049 Å °
Refinement TLS groupSelection details: all

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