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- PDB-2val: Crystal structure of an Escherichia coli tRNAGly microhelix at 2.... -

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Basic information

Entry
Database: PDB / ID: 2val
TitleCrystal structure of an Escherichia coli tRNAGly microhelix at 2.0 Angstrom resolution
Components
  • 5'-R(*GP*CP*GP*GP*GP*AP*AP)-3'
  • 5'-R(*UP*UP*CP*CP*CP*GP*CP)-3'
KeywordsRNA / GLYCYL-TRNA SYNTHETASE (GLYRS) SYSTEM / TRNAGLY ACCEPTOR STEM MICROHELIX / RNA TRNA IDENTITY ELEMENTS / MAGNESIUM BINDING SITES
Function / homologyRNA
Function and homology information
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsForster, C. / Brauer, A.B.E. / Perbandt, M. / Lehmann, D. / Furste, J.P. / Betzel, C. / Erdmann, V.A.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: Crystal Structure of an Escherichia Coli Trnagly Microhelix at 2.0 Angstrom Resolution
Authors: Forster, C. / Brauer, A.B.E. / Perbandt, M. / Lehmann, D. / Furste, J.P. / Betzel, C. / Erdmann, V.A.
History
DepositionSep 3, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 16, 2019Group: Data collection / Other / Category: pdbx_database_status / reflns / reflns_shell
Item: _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.5May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: 5'-R(*GP*CP*GP*GP*GP*AP*AP)-3'
B: 5'-R(*GP*CP*GP*GP*GP*AP*AP)-3'
C: 5'-R(*UP*UP*CP*CP*CP*GP*CP)-3'
D: 5'-R(*UP*UP*CP*CP*CP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8905
Polymers8,8664
Non-polymers241
Water1,00956
1
A: 5'-R(*GP*CP*GP*GP*GP*AP*AP)-3'
C: 5'-R(*UP*UP*CP*CP*CP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,4573
Polymers4,4332
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint0 kcal/mol
Surface area3370 Å2
MethodPQS
2
B: 5'-R(*GP*CP*GP*GP*GP*AP*AP)-3'
D: 5'-R(*UP*UP*CP*CP*CP*GP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)4,4332
Polymers4,4332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint0 kcal/mol
Surface area3310 Å2
MethodPQS
Unit cell
Length a, b, c (Å)35.348, 35.348, 130.821
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-2010-

HOH

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Components

#1: RNA chain 5'-R(*GP*CP*GP*GP*GP*AP*AP)-3' / E.COLI TRNAGLY MICROHELIX


Mass: 2299.459 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli)
#2: RNA chain 5'-R(*UP*UP*CP*CP*CP*GP*CP)-3' / E.COLI TRNAGLY MICROHELIX


Mass: 2133.307 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.68 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growDetails: 50 MM SODIUM CACODYLATE, PH 6.0, 10 MM SPERMINE, 10 MM MAGNESIUM SULFATE, 2.0 M AMMONIUM SULFATE, 0.5 MM RNA, ROOM TEMPERATUE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8063
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8063 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 6908 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 34
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 5.8 / % possible all: 83.4

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Processing

Software
NameVersionClassification
REFMAC5refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→17.67 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.318 -5 %RANDOM
Rwork0.241 ---
obs-9123 99.1 %-
Refinement stepCycle: LAST / Resolution: 2→17.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 586 1 56 643

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