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- PDB-1t0e: Crystal Structure of 2-aminopurine labelled bacterial decoding si... -

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Basic information

Entry
Database: PDB / ID: 1t0e
TitleCrystal Structure of 2-aminopurine labelled bacterial decoding site RNA
Components
  • 5'-R(*CP*GP*AP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*CP*C)-3'
  • 5'-R(*GP*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*UP*CP*GP*G)-3'
KeywordsRNA / BACTERIAL DECODING SITE RNA / 9-beta-D-Ribofuranosyl-9H-purin-2-amine
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsShandrick, S. / Zhao, Q. / Han, Q. / Ayida, B.K. / Takahashi, M. / Winters, G.C. / Simonsen, K.B. / Vourloumis, D. / Hermann, T.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2004
Title: Monitoring molecular recognition of the ribosomal decoding site.
Authors: Shandrick, S. / Zhao, Q. / Han, Q. / Ayida, B.K. / Takahashi, M. / Winters, G.C. / Simonsen, K.B. / Vourloumis, D. / Hermann, T.
History
DepositionApr 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 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: 5'-R(*GP*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*UP*CP*GP*G)-3'
C: 5'-R(*CP*GP*AP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4134
Polymers11,2212
Non-polymers1922
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.040, 32.950, 92.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 5860.515 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain 5'-R(*CP*GP*AP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*CP*C)-3'


Mass: 5360.284 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.1 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Ammonium sulfate, magnesium acetate, cacodylate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ammonium sulfate11
2magnesium acetate11
3cacodylate11

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 7, 2003 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 11356 / Num. obs: 11015 / % possible obs: 97 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 14.9 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 32.7
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 6.15 / Num. unique all: 902 / % possible all: 81.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: solved the construct model

Resolution: 1.7→8 Å / Isotropic thermal model: anistropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1096 -random
Rwork0.209 ---
obs0.2271 10711 95.5 %-
all-11221 --
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.952 Å20 Å20 Å2
2--0.522 Å20 Å2
3---0.429 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 809 10 130 949
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.022
X-RAY DIFFRACTIONc_angle_d1.9
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.028
RfactorNum. reflection% reflection
Rfree0.334 144 -
Rwork0.298 --
obs--81.5 %

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