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- PDB-2v6w: tRNASer acceptor stem: Conformation and hydration of a microhelix... -

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Basic information

Entry
Database: PDB / ID: 2v6w
TitletRNASer acceptor stem: Conformation and hydration of a microhelix in a crystal structure at 1.8 Angstrom resolution
Components
  • 5'-R(*GP*GP*AP*GP*AP*GP*AP)-3'
  • 5'-R(*UP*CP*UP*CP*UP*CP*CP)-3'
KeywordsRNA / E.COLI TRNASER ACCEPTOR STEM MICROHELIX / NUCLEIC ACID TRNA IDENTITY / 1.8 ANGSTROM RESOLUTION / HYDRATION PATTERN
Function / homologyRNA
Function and homology information
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFoerster, C. / Brauer, A.B.E. / Brode, S. / Fuerste, J.P. / Betzel, C. / Erdmann, V.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Trnaser Acceptor Stem: Conformation and Hydration of a Microhelix in a Crystal Structure at 1.8 A Resolution.
Authors: Forster, C. / Brauer, A.B.E. / Brode, S. / Furste, J.P. / Betzel, C. / Erdmann, V.A.
History
DepositionJul 23, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*GP*GP*AP*GP*AP*GP*AP)-3'
B: 5'-R(*UP*CP*UP*CP*UP*CP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)4,4182
Polymers4,4182
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint0 kcal/mol
Surface area3100 Å2
MethodPQS
Unit cell
Length a, b, c (Å)36.100, 38.920, 30.790
Angle α, β, γ (deg.)90.00, 110.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain 5'-R(*GP*GP*AP*GP*AP*GP*AP)-3'


Mass: 2323.483 Da / Num. of mol.: 1 / Fragment: ACCEPTOR STEM MICROHELIX / Source method: obtained synthetically / Details: TRNA-SER MICROHELIX / Source: (synth.) ESCHERICHIA COLI (E. coli)
#2: RNA chain 5'-R(*UP*CP*UP*CP*UP*CP*CP)-3'


Mass: 2094.267 Da / Num. of mol.: 1 / Fragment: ACCEPTOR STEM MICROHELIX / Source method: obtained synthetically / Details: TRNA-SER MICROHELIX / Source: (synth.) ESCHERICHIA COLI (E. coli)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growTemperature: 294 K
Details: 50 MM SODIUM CACODYLATE, PH 6.0, 15 MM MAGNESIUM SULFATE, 1.8 M LITHIUM SULFATE, 294 K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→80 Å / Num. obs: 3677 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.9

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Processing

SoftwareName: REFMAC / Version: 5 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→80 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflection
Rwork0.154 --
obs-3494 98.9 %
Refinement stepCycle: LAST / Resolution: 1.8→80 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 292 0 75 367

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