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- PDB-1l3d: Low Resolution Crystal Structure of a Viral RNA Pseudoknot -

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Basic information

Entry
Database: PDB / ID: 1l3d
TitleLow Resolution Crystal Structure of a Viral RNA Pseudoknot
ComponentsRNA pseudoknot
KeywordsRNA / Pseudoknot / frameshifting / viral RNA / flexibility
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsEgli, M. / Minasov, G. / Su, L. / Rich, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Metal ions and flexibility in a viral RNA pseudoknot at atomic resolution.
Authors: Egli, M. / Minasov, G. / Su, L. / Rich, A.
History
DepositionFeb 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA pseudoknot


Theoretical massNumber of molelcules
Total (without water)9,2451
Polymers9,2451
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.810, 107.810, 107.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: RNA chain RNA pseudoknot


Mass: 9245.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA SEQUENCE TAKEN FROM BEET WESTERN YELLOW VIRUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 5.65 Å3/Da / Density % sol: 78.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: ammonium sulfate, sodium citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2sodium citrate11
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.7 mg/mlRNA1drop
21 Mammonium sulfate1drop
333 mMsodium citrate1droppH5.0
42 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 17, 1997 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.85→30 Å / Num. all: 5034 / Num. obs: 5034 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.2 % / Biso Wilson estimate: 63.1 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 39.5
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 9.3 / Num. unique all: 486 / % possible all: 100
Reflection
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 437D

437d


Resolution: 2.85→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: G. Parkinson et al., Acta Cryst. (1996) D52, 57-64
Details: Crystallographic conjugate gradient minimization refinement using maximum likelihood target for amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.275 514 -RANDOM
Rwork0.271 ---
all-4989 --
obs-4989 99.7 %-
Displacement parametersBiso mean: 43.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.768 Å20 Å20 Å2
2--1.768 Å20 Å2
3---1.768 Å2
Refinement stepCycle: LAST / Resolution: 2.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 677 0 14 691
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1
LS refinement shellResolution: 2.85→2.98 Å
RfactorNum. reflection% reflection
Rfree0.443 65 -
Rwork0.427 --
obs--99.7 %
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.271
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1
LS refinement shell
*PLUS
Rfactor obs: 0.427

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