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- PDB-2xsl: The crystal structure of a Thermus thermophilus tRNAGly acceptor ... -

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Basic information

Entry
Database: PDB / ID: 2xsl
TitleThe crystal structure of a Thermus thermophilus tRNAGly acceptor stem microhelix at 1.6 Angstroem resolution
Components
  • 5'-R(*CP*UP*CP*CP*CP*GP*C)-3'
  • 5'-R(*GP*CP*GP*GP*GP*AP*G)-3'
KeywordsRNA / IDENTITY ELEMENTS / GLYCYL-TRNA SYNTHETASE (GLYRS) / RNA HYDRATION
Function / homology: / RNA
Function and homology information
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsOberthuer, D. / Eichert, A. / Erdmann, V.A. / Fuerste, J.P. / Betzel, C. / Foerster, C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: The Crystal Structure of a Thermus Thermophilus tRNA(Gly) Acceptor Stem Microhelix at 1.6 A Resolution.
Authors: Oberthur, D. / Eichert, A. / Erdmann, V.A. / Furste, J.P. / Betzel, C. / Forster, C.
History
DepositionOct 29, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)8,8964
Polymers8,8964
Non-polymers00
Water1,58588
1
A: 5'-R(*GP*CP*GP*GP*GP*AP*G)-3'
B: 5'-R(*CP*UP*CP*CP*CP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)4,4482
Polymers4,4482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-4.4 kcal/mol
Surface area2760 Å2
MethodPISA
2
C: 5'-R(*GP*CP*GP*GP*GP*AP*G)-3'
D: 5'-R(*CP*UP*CP*CP*CP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)4,4482
Polymers4,4482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-3.8 kcal/mol
Surface area2750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.187, 29.015, 29.534
Angle α, β, γ (deg.)107.17, 97.37, 96.55
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 7
2111C1 - 7
1121B8 - 14
2121D8 - 14

NCS ensembles :
ID
1
2

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Components

#1: RNA chain 5'-R(*GP*CP*GP*GP*GP*AP*G)-3' / TRNAGLY


Mass: 2315.459 Da / Num. of mol.: 2 / Fragment: MICROHELIX, RESIDUES 1-7 / Source method: obtained synthetically / Source: (synth.) THERMUS THERMOPHILUS (bacteria) / References: GenBank: 55979969
#2: RNA chain 5'-R(*CP*UP*CP*CP*CP*GP*C)-3' / TRNAGLY


Mass: 2132.323 Da / Num. of mol.: 2 / Fragment: MICROHELIX, RESIDUES 66-72 / Source method: obtained synthetically / Source: (synth.) THERMUS THERMOPHILUS (bacteria) / References: GenBank: 55979969
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.52 Å3/Da / Density % sol: 62.59 % / Description: NONE
Crystal growpH: 7
Details: 0.5 MM RNA IN 40 MM SODIUM CACODYLATE, PH 7.0, 12 MM SPERMINE TETRA-HCL, 80 MM NACL AND 10 % (V/V) MPD, EQUILIBRATED AGAINST 35 % (V/V) MPD, ROOM TEMPERATURE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123
DetectorType: MARRESEARCH SX-165 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.6→36 Å / Num. obs: 10142 / % possible obs: 94.7 % / Observed criterion σ(I): 1.7 / Redundancy: 3.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.5
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.7 / % possible all: 72.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ARTIFICIAL RNA

Resolution: 1.59→27.8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.032 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28033 485 4.8 %RANDOM
Rwork0.2369 ---
obs0.23898 9648 93.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.03 Å2-0.03 Å2
2---0.02 Å2-0.01 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.59→27.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 588 0 88 676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.021654
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.13831014
X-RAY DIFFRACTIONr_angle_other_deg
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_restr0.1090.2112
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.02292
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.1493654
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4964.51014
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A154tight positional0.20.05
11B154tight positional0.20.05
21B140tight positional0.240.05
22D140tight positional0.240.05
11A154tight thermal0.550.5
11B154tight thermal0.550.5
21B140tight thermal0.770.5
22D140tight thermal0.770.5
LS refinement shellResolution: 1.594→1.636 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.444 23 -
Rwork0.453 483 -
obs--62.62 %

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