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- PDB-387d: RNA Pseudoknot with 3D Domain Swapping -

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Basic information

Entry
Database: PDB / ID: 387d
TitleRNA Pseudoknot with 3D Domain Swapping
ComponentsRNA Pseudoknot
KeywordsRNA / RNA PSEUDOKNOT
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 3.1 Å
AuthorsLietzke, S.E. / Kundrot, C.E. / Barnes, C.L.
Citation
Journal: Structure, Motion, Interaction and Expression of Biological Macromolecules, The Proceedings of the Tenth Conversation held at The University-SUNY, Albany NY, June 17-21, 1997
Year: 1998
Title: The Structure of an RNA Pseudoknot Shows 3D Domain Swapping
Authors: Lietzke, S.E. / Barnes, C.L. / Malone, V.F. / Jones, J.T. / Kundrot, C.E.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Preliminary X-ray Diffraction Studies of an RNA Pseudoknot that Inhibits HIV-1 Reverse Transcriptase
Authors: Jones, J.T. / Barnes, C.L. / Lietzke, S.E. / Wieichenrieder, O. / Doudna, J.A. / Kundrot, C.E.
#2: Journal: J.Mol.Biol. / Year: 1995
Title: Comprehensive chemical modification interference and nucleotide substitution analysis of an RNA pseudoknot inhibitor to HIV-1 reverse transcriptase
Authors: Green, L. / Waugh, S. / Brinkley, J.P. / Hostomska, Z. / Tuerk, C.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: RNA pseudoknots that inhibit human immunodeficiency
Authors: Tuerk, C. / MacDougal, S. / Gould, L.
History
DepositionApr 14, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 27, 2023Group: 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: RNA Pseudoknot


Theoretical massNumber of molelcules
Total (without water)8,3901
Polymers8,3901
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.600, 61.600, 98.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Cell settingtetragonal
Space group name H-MP4322

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Components

#1: RNA chain RNA Pseudoknot


Mass: 8390.091 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 26-mer / Keywords: RNA
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 5.59 Å3/Da / Density % sol: 78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K
Components of the solutions
IDConc.NameCrystal-IDDetailsSol-IDVolume (Å3)
12MGCL21311
25SODIUM CACODYLATE1614
38SODIUM ACETATE1917
411SODIUM CACODYLATE112210
514SODIUM ACETATE115213

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Oct 26, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 3615 / Num. obs: 3615 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.051

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
X-PLOR3.1refinement
XDSdata reduction
RefinementResolution: 3.1→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.234 254 7.3 %
Rwork0.181 --
obs0.1811 3467 -
Refinement stepCycle: LAST / Resolution: 3.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 639 0 18 657
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.61
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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