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- PDB-9j4o: Crystal structure of B. subtilis Leucine tRNA with UAA anticodon -

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Basic information

Entry
Database: PDB / ID: 9j4o
TitleCrystal structure of B. subtilis Leucine tRNA with UAA anticodon
ComponentsLeucine tRNA_UAA (89-MER)
KeywordsRNA / tRNA
Function / homologySPERMINE / : / RNA / RNA (> 10)
Function and homology information
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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_UAA (89-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9512
Polymers28,7491
Non-polymers2021
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.190, 37.200, 81.990
Angle α, β, γ (deg.)90.00, 99.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain Leucine tRNA_UAA (89-MER)


Mass: 28749.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Plasmid: pBSTNAV / Production host: Escherichia coli K-12 (bacteria) / References: GenBank: 1837880844
#2: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
Has ligand of interestN
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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.072 M sodium chloride, 0.036 M sodium cacodylate trihydrate pH 7.0, 27% v/v (+/-)-2-methyl-2,4-pentanediol, 0.0108 M spermine tetrahydrochloride, 0.5% v/v ethyl acetate

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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: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: May 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.499→33.796 Å / Num. obs: 8962 / % possible obs: 91.6 % / Redundancy: 6.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.05 / Rrim(I) all: 0.123 / Net I/σ(I): 9.7
Reflection shellResolution: 2.499→2.542 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.945 / Mean I/σ(I) obs: 1 / Num. unique obs: 462 / CC1/2: 0.62 / Rpim(I) all: 0.839 / Rrim(I) all: 2.123 / % possible all: 99.6

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Processing

Software
NameVersionClassification
MxDCdata collection
autoPROCdata processing
autoPROCdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
REFMAC5.8.0430refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→33.796 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 14.859 / SU ML: 0.295 / Cross valid method: THROUGHOUT / ESU R: 0.784 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26328 459 5.1 %RANDOM
Rwork0.21626 ---
obs0.21861 8502 91.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.492 Å2
Baniso -1Baniso -2Baniso -3
1--4.72 Å20 Å2-1.17 Å2
2---3.19 Å20 Å2
3---7.87 Å2
Refinement stepCycle: 1 / Resolution: 2.5→33.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1866 14 0 1880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0112099
X-RAY DIFFRACTIONr_bond_other_d0.0020.019882
X-RAY DIFFRACTIONr_angle_refined_deg1.8991.843263
X-RAY DIFFRACTIONr_angle_other_deg0.5351.6662134
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_restr0.0660.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021054
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02334
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_it5.4095.9162099
X-RAY DIFFRACTIONr_scbond_other5.4085.9162100
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.85110.7543264
X-RAY DIFFRACTIONr_long_range_B_refined9.30774.552820
X-RAY DIFFRACTIONr_long_range_B_other9.30574.542821
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.563 Å
RfactorNum. reflection% reflection
Rfree0.494 39 -
Rwork0.404 676 -
obs--99.31 %

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