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- PDB-3p59: First Crystal Structure of a RNA Nanosquare -

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Basic information

Entry
Database: PDB / ID: 3p59
TitleFirst Crystal Structure of a RNA Nanosquare
Components
  • RNA (5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*(5BU)P*G)-3')
  • RNA (5'-R(*CP*CP*GP*GP*CP*AP*GP*CP*CP*U)-3')
KeywordsRNA / RNA square
Function / homologyCOBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1793 Å
AuthorsDibrov, S. / Hermann, T. / McLean, J. / Parsons, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Self-assembling RNA square.
Authors: Dibrov, S.M. / McLean, J. / Parsons, J. / Hermann, T.
History
DepositionOct 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 (5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*(5BU)P*G)-3')
B: RNA (5'-R(*CP*CP*GP*GP*CP*AP*GP*CP*CP*U)-3')
C: RNA (5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*(5BU)P*G)-3')
D: RNA (5'-R(*CP*CP*GP*GP*CP*AP*GP*CP*CP*U)-3')
E: RNA (5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*(5BU)P*G)-3')
F: RNA (5'-R(*CP*CP*GP*GP*CP*AP*GP*CP*CP*U)-3')
G: RNA (5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*(5BU)P*G)-3')
H: RNA (5'-R(*CP*CP*GP*GP*CP*AP*GP*CP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,90720
Polymers32,2478
Non-polymers1,66012
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.378, 62.378, 126.268
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11H-24-

HOH

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Components

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


Mass: 4909.849 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Chemically Synthesized
#2: RNA chain
RNA (5'-R(*CP*CP*GP*GP*CP*AP*GP*CP*CP*U)-3')


Mass: 3151.940 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Chemically Synthesized
#3: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CoH18N6
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 150 mM magnesium chloride, 50 mM sodium cacodylate, 10mM hexamminecobalt (III) chloride, 50 mM KCl, 17% PEG 400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9202752 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202752 Å / Relative weight: 1
ReflectionResolution: 2.157→25.06 Å / Num. obs: 25640 / % possible obs: 86.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 30.2 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 49.5
Reflection shellResolution: 2.157→2.27 Å / Redundancy: 2 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2 / Num. unique all: 946 / % possible all: 30

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1793→25.059 Å / σ(F): 1.99 / Phase error: 20.61 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1295 5.05 %RANDOM
Rwork0.1556 ---
obs0.157 25640 86.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.4 Å2 / ksol: 0.361 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1793→25.059 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2074 72 118 2264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082372
X-RAY DIFFRACTIONf_angle_d1.1143741
X-RAY DIFFRACTIONf_dihedral_angle_d21.6871141
X-RAY DIFFRACTIONf_chiral_restr0.058478
X-RAY DIFFRACTIONf_plane_restr0.00998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1793-2.26650.2808660.273946X-RAY DIFFRACTION30
2.2665-2.36950.30791160.26832158X-RAY DIFFRACTION67
2.3695-2.49440.25821510.24083019X-RAY DIFFRACTION94
2.4944-2.65050.31941510.24133002X-RAY DIFFRACTION95
2.6505-2.85490.28412030.22552993X-RAY DIFFRACTION94
2.8549-3.14160.17771410.17173040X-RAY DIFFRACTION95
3.1416-3.59510.15611490.13943043X-RAY DIFFRACTION95
3.5951-4.52490.16421450.11523039X-RAY DIFFRACTION95
4.5249-24.83480.16451460.11863042X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 17.6206 Å / Origin y: -26.3046 Å / Origin z: 10.6335 Å
111213212223313233
T0.1072 Å2-0.0039 Å2-0.0231 Å2-0.1453 Å2-0.04 Å2--0.0085 Å2
L0.3323 °20.2191 °20.0498 °2-0.4423 °20.1218 °2---0.443 °2
S0.0279 Å °0.0525 Å °0.0085 Å °-0.0279 Å °0.1192 Å °-0.0171 Å °0.0807 Å °-0.0062 Å °0.148 Å °
Refinement TLS groupSelection details: all

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