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- PDB-6ugj: Crystal structure of a fragment of E. coli tRNA(Asp) consisting o... -

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Basic information

Entry
Database: PDB / ID: 6ugj
TitleCrystal structure of a fragment of E. coli tRNA(Asp) consisting of its acceptor stem/T stem-loop. Short unit cell.
ComponentstRNA(Asp) acceptor stem/T stem-loop
KeywordsRNA / tRNA RNA unmodified T-loop acceptor stem
Function / homologyDIPHOSPHATE / URACIL / RNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChan, C.W. / Mondragon, A.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 GM058443 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R35 GM118108 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)T32 GM008152 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)T32 GM008382 United States
CitationJournal: Rna / Year: 2020
Title: Crystal structures of an unmodified bacterial tRNA reveal intrinsic structural flexibility and plasticity as general properties of unbound tRNAs.
Authors: Chan, C.W. / Badong, D. / Rajan, R. / Mondragon, A.
History
DepositionSep 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA(Asp) acceptor stem/T stem-loop
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3724
Polymers9,9901
Non-polymers3823
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-2 kcal/mol
Surface area5610 Å2
Unit cell
Length a, b, c (Å)43.845, 43.845, 259.285
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-101-

SO4

21A-215-

HOH

31A-220-

HOH

41A-243-

HOH

51A-247-

HOH

61A-248-

HOH

71A-252-

HOH

81A-254-

HOH

91A-261-

HOH

101A-266-

HOH

111A-270-

HOH

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Components

#1: RNA chain tRNA(Asp) acceptor stem/T stem-loop


Mass: 9989.942 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N2O2
#4: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.4 Å3/Da / Density % sol: 48.76 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / Details: 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Ambient temp details: Crystals were flash frozen with liquid nitrogen in crystallization well solution supplemented with either increased ammonium sulfate concentration or with 20% (v/v) glycerol for cryo-protection
Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 1, 2017 / Details: Monochromator
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.6→43.25 Å / Num. obs: 9777 / % possible obs: 92 % / Redundancy: 21.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.034 / Rrim(I) all: 0.16 / Net I/σ(I): 11.5
Reflection shellResolution: 1.6→1.691 Å / Redundancy: 14.3 % / Rmerge(I) obs: 4.054 / Mean I/σ(I) obs: 1 / Num. unique obs: 6865 / CC1/2: 0.492 / Rpim(I) all: 1.089 / Rrim(I) all: 4.2 / % possible all: 68.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5 base pair A-form RNA helix

Resolution: 1.6→43.25 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.275 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.137
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2724 492 5.1 %RANDOM
Rwork0.2136 ---
obs0.2165 9077 72.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 118.83 Å2 / Biso mean: 35.743 Å2 / Biso min: 19.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å2-0 Å2
2---0.1 Å2-0 Å2
3---0.32 Å2
Refinement stepCycle: final / Resolution: 1.6→43.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 600 22 70 692
Biso mean--79.68 38.2 -
Num. residues----28
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.011689
X-RAY DIFFRACTIONr_bond_other_d0.0020.02279
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.2921071
X-RAY DIFFRACTIONr_angle_other_deg1.5932.985675
X-RAY DIFFRACTIONr_chiral_restr0.0750.2112
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02346
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02157
LS refinement shellResolution: 1.602→1.644 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 7 -
Rwork0.399 187 -
all-194 -
obs--20.1 %

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