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- PDB-6ugg: Structure of unmodified E. coli tRNA(Asp) -

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Basic information

Entry
Database: PDB / ID: 6ugg
TitleStructure of unmodified E. coli tRNA(Asp)
ComponentstRNAasp
KeywordsRNA / tRNA RNA unmodified
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNAasp
B: tRNAasp


Theoretical massNumber of molelcules
Total (without water)49,6312
Polymers49,6312
Non-polymers00
Water41423
1
A: tRNAasp


Theoretical massNumber of molelcules
Total (without water)24,8161
Polymers24,8161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: tRNAasp


Theoretical massNumber of molelcules
Total (without water)24,8161
Polymers24,8161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.677, 64.677, 195.799
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: RNA chain tRNAasp


Mass: 24815.684 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: GenBank: 1710318528
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.38 Å3/Da / Density % sol: 48.36 %
Description: Clusters of arrow-like crystals. Single crystals excised from cluster.
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 uL 20 mg/ml E. coli tRNA(Asp) + 2 uL equilibration solution (50 mM sodium cacodylate, pH 7.5, 30% MPD, 10 mM spermine tetrahydrochloride, 300 mM sodium chloride, 300 mM potassium chloride) ...Details: 2 uL 20 mg/ml E. coli tRNA(Asp) + 2 uL equilibration solution (50 mM sodium cacodylate, pH 7.5, 30% MPD, 10 mM spermine tetrahydrochloride, 300 mM sodium chloride, 300 mM potassium chloride) + 0.5 uL 0.25% w/v p-coumaric acid, 0.25% w/v phenylurea, 0.25% w/v poly(3-hydroxybutyric acid), 0.25% w/v sulfaguanidine, 0.02 M sodium HEPES, pH 6.8

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Data collection

DiffractionMean temperature: 100 K
Ambient temp details: Crystals were flash frozen directly in mother liquor with liquid nitrogen
Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0782 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 14, 2017 / Details: Monochromator
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0782 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.524
11-K, -H, -L20.476
ReflectionResolution: 1.95→48.62 Å / Num. obs: 35638 / % possible obs: 94 % / Redundancy: 30 % / CC1/2: 0.992 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.029 / Rrim(I) all: 0.158 / Net I/σ(I): 15.8
Reflection shellResolution: 1.95→2.056 Å / Redundancy: 33.7 % / Rmerge(I) obs: 2.683 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 55102 / CC1/2: 0.488 / Rpim(I) all: 0.468 / Rrim(I) all: 2.724 / % possible all: 50.8

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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: PDB entry 1EHZ

1ehz


Resolution: 1.95→48.62 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.442 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.035
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 1469 4.7 %RANDOM
Rwork0.2154 ---
obs0.2164 30070 88.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 123.64 Å2 / Biso mean: 50.999 Å2 / Biso min: 22.58 Å2
Baniso -1Baniso -2Baniso -3
1-2.3 Å20 Å20 Å2
2--2.3 Å20 Å2
3----4.59 Å2
Refinement stepCycle: final / Resolution: 1.95→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3288 0 23 3311
Biso mean---36.61 -
Num. residues----154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0113670
X-RAY DIFFRACTIONr_bond_other_d0.0020.021506
X-RAY DIFFRACTIONr_angle_refined_deg0.851.285722
X-RAY DIFFRACTIONr_angle_other_deg1.29833662
X-RAY DIFFRACTIONr_chiral_restr0.070.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021832
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02822
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.502 13 -
Rwork0.286 262 -
all-275 -
obs--10.53 %

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