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- PDB-1f27: CRYSTAL STRUCTURE OF A BIOTIN-BINDING RNA PSEUDOKNOT -

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Basic information

Entry
Database: PDB / ID: 1f27
TitleCRYSTAL STRUCTURE OF A BIOTIN-BINDING RNA PSEUDOKNOT
Components
  • RNA (5'-R(*AP*AP*AP*AP*AP*GP*UP*CP*CP*UP*C)-3')
  • RNA (5'-R(*AP*CP*CP*GP*UP*CP*AP*GP*AP*GP*GP*AP*CP*AP*CP*GP*GP*UP*U)-3')
KeywordsRNA / RNA APTAMER / PSEUDOKNOT / BIOTIN-BINDING RNA
Function / homologyBIOTIN / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.3 Å
AuthorsNix, J. / Sussman, D. / Wilson, C.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: The 1.3 A crystal structure of a biotin-binding pseudoknot and the basis for RNA molecular recognition.
Authors: Nix, J. / Sussman, D. / Wilson, C.
History
DepositionMay 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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_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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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.ptnr2_symmetry / _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 (5'-R(*AP*CP*CP*GP*UP*CP*AP*GP*AP*GP*GP*AP*CP*AP*CP*GP*GP*UP*U)-3')
B: RNA (5'-R(*AP*AP*AP*AP*AP*GP*UP*CP*CP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9819
Polymers9,5912
Non-polymers3907
Water3,315184
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.59, 30.96, 62.11
Angle α, β, γ (deg.)90, 111.88, 90
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-197-

HOH

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Components

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


Mass: 6116.713 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SEQUENCE FROM IN VITRO SELECTION EXPERIMENT
#2: RNA chain RNA (5'-R(*AP*AP*AP*AP*AP*GP*UP*CP*CP*UP*C)-3')


Mass: 3474.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA BIOTIN-BINDING APTAMER
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 301 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: MPD, POTASIUM HEPES, MGCL2, KCL, BIOTIN, SPERMINE, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 301K
Components of the solutions
IDNameCrystal-IDSol-ID
1POTASIUM HEPES11
2MGCL211
3KCL11
4BIOTIN11
5SPERMINE11
6MPD11
7MPD12
Crystal grow
*PLUS
Temperature: 28 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mg/mlRNA1drop
23.3 %MPD1drop
313.3 mMpotassium caodylate1drop
46.6 mMpotassium HEPES1drop
50.1 mMspermine1drop
63.5 mM1dropMgCl2
73.5 mMbiotin1drop
822.5 %MPD1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)Wavelength
SYNCHROTRONALS 5.0.210.97186, 0.97954, 0.97969, 0.98743
SYNCHROTRONALS 5.0.220.965
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDSep 20, 1998
ADSC QUANTUM 42CCDMar 21, 1999
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.971861
20.979541
30.979691
40.987431
50.9651
ReflectionResolution: 1.3→18 Å / Num. all: 20852 / % possible obs: 92 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6.3 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 9
Reflection shellResolution: 1.3→1.38 Å / Rmerge(I) obs: 0.38 / % possible all: 66.4
Reflection
*PLUS
Num. obs: 20852 / Num. measured all: 130824
Reflection shell
*PLUS
% possible obs: 66.4 %

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.3→17.18 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1797 8.6 %RANDOM
Rwork0.199 ---
obs0.199 20852 91.7 %-
Refinement stepCycle: LAST / Resolution: 1.3→17.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 634 22 184 840
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.77

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