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- PDB-9j4n: Crystal structure of E. coli Leucine tRNA with UAG anticodon -

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Basic information

Entry
Database: PDB / ID: 9j4n
TitleCrystal structure of E. coli Leucine tRNA with UAG anticodon
ComponentsLeucine tRNA_UAG (85-MER)
KeywordsRNA / tRNA
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKim, J. / Cho, G.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Rna / Year: 2025
Title: Crystal structures of free-state tRNA Leu reveal conformational flexibility of type-II tRNAs.
Authors: Cho, G. / Yoo, J. / Shin, K. / Lee, J. / Lim, J. / Kim, J.
History
DepositionAug 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leucine tRNA_UAG (85-MER)


Theoretical massNumber of molelcules
Total (without water)27,4411
Polymers27,4411
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.365, 114.179, 53.817
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: RNA chain Leucine tRNA_UAG (85-MER)


Mass: 27441.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Plasmid: pBSTNAV / Production host: Escherichia coli K-12 (bacteria) / References: GenBank: 1845258627
Has protein modificationN

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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: 3.44 Å3/Da / Density % sol: 64.2 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.25 M ammonium sulfate, 0.1 M sodium acetate trihydrate, pH 4.6, 32% (w/v) polyethylene glycol monomethyl ether 2000
Temp details: RT

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: LN2 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.897→48.681 Å / Num. obs: 4225 / % possible obs: 86.8 % / Redundancy: 11.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.059 / Rrim(I) all: 0.2 / Net I/σ(I): 11.1
Reflection shellResolution: 2.897→3.331 Å / Redundancy: 13.2 % / Rmerge(I) obs: 1.75 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 352 / CC1/2: 0.626 / Rpim(I) all: 0.498 / Rrim(I) all: 1.821 / % possible all: 61.7

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
autoPROCdata processing
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
REFMAC5.8.0425refinement
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→48.681 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.895 / Cross valid method: THROUGHOUT / ESU R Free: 0.67 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26961 218 5.2 %RANDOM
Rwork0.24644 ---
obs0.24762 4000 48.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.52 Å2
Baniso -1Baniso -2Baniso -3
1--3.27 Å2-0 Å2-0 Å2
2---0.09 Å20 Å2
3---3.36 Å2
Refinement stepCycle: 1 / Resolution: 2.9→48.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1737 0 0 1737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0111940
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.681.8383021
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02845
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.3998.4231940
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined20.927116.599654
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.186 1 -
Rwork0.446 24 -
obs--4.49 %

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