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- PDB-437d: CRYSTAL STRUCTURE OF AN RNA PSEUDOKNOT FROM BEET WESTERN YELLOW V... -

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Basic information

Entry
Database: PDB / ID: 437d
TitleCRYSTAL STRUCTURE OF AN RNA PSEUDOKNOT FROM BEET WESTERN YELLOW VIRUS INVOLVED IN RIBOSOMAL FRAMESHIFTING
ComponentsRNA PSEUDOKNOT
KeywordsRNA / PSEUDOKNOT / TRIPLEX / VIRAL FRAMESHIFTING
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsSu, L. / Chen, L. / Egli, M. / Berger, J.M. / Rich, A.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot.
Authors: Su, L. / Chen, L. / Egli, M. / Berger, J.M. / Rich, A.
History
DepositionNov 24, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Dec 3, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA PSEUDOKNOT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2933
Polymers9,2451
Non-polymers472
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.080, 30.080, 140.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Cell settingtrigonal
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-118-

HOH

21A-122-

HOH

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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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 1.98 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MGCL211
22-BUTANOL11
3POTASSIUM MOPS11
4SPERMIDINE11
52-BUTANOL12
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mg/mlRNA1drop
25 mM1dropMgCl2
35 %sec-butanol1drop
4100 mMpotassium MOPS1drop
52 mMspermidine1drop
618 %sec-butanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.1406
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jun 14, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1406 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 9806 / Num. obs: 8793 / % possible obs: 93 % / Observed criterion σ(F): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.07
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.165 / % possible all: 70
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 69.9 % / Mean I/σ(I) obs: 3.5

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Processing

Software
NameClassification
MIRASmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.6→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.254 916 9 %
Rwork0.207 --
obs0.207 7877 85 %
all-9806 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.456 Å2-0.282 Å20 Å2
2---2.456 Å20 Å2
3---4.911 Å2
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 640 2 124 766
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.87
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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