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- PDB-5c5w: 1.25 A resolution structure of an RNA 20-mer -

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Basic information

Entry
Database: PDB / ID: 5c5w
Title1.25 A resolution structure of an RNA 20-mer
ComponentsRNA (5'-R(P*CP*CP*UP*GP*AP*GP*UP*UP*CP*AP*AP*UP*UP*CP*UP*AP*GP*CP*G)-3')
KeywordsRNA / duplex / C-C / A-C / G-U base pairing
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesSaccharomyces (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.25 Å
AuthorsStewart, M. / Valkov, E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105178939 United Kingdom
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: 1.25 angstrom resolution structure of an RNA 20-mer that binds to the TREX2 complex.
Authors: Valkov, E. / Stewart, M.
History
DepositionJun 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 8, 2024Group: 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 (5'-R(P*CP*CP*UP*GP*AP*GP*UP*UP*CP*AP*AP*UP*UP*CP*UP*AP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,0161
Polymers6,0161
Non-polymers00
Water1,74797
1
A: RNA (5'-R(P*CP*CP*UP*GP*AP*GP*UP*UP*CP*AP*AP*UP*UP*CP*UP*AP*GP*CP*G)-3')

A: RNA (5'-R(P*CP*CP*UP*GP*AP*GP*UP*UP*CP*AP*AP*UP*UP*CP*UP*AP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)12,0312
Polymers12,0312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+11
Buried area1720 Å2
ΔGint-10 kcal/mol
Surface area7240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.870, 39.870, 156.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-10-

C

21A-116-

HOH

31A-118-

HOH

41A-121-

HOH

51A-124-

HOH

61A-125-

HOH

71A-148-

HOH

81A-167-

HOH

91A-171-

HOH

101A-173-

HOH

111A-186-

HOH

121A-197-

HOH

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Components

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


Mass: 6015.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces (fungus)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: See manuscript for details. 2M ammonium sulphate, 0.2 M NaCl, 0.1 M cacodylate buffer.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.25→52.29 Å / Num. obs: 13567 / % possible obs: 100 % / Redundancy: 23.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 21.5
Reflection shellResolution: 1.25→1.28 Å / Rmerge(I) obs: 1.383 / Mean I/σ(I) obs: 1.6 / % possible all: 89.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.25→52.29 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 22.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1879 667 4.92 %
Rwork0.1794 --
obs0.1798 13563 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→52.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 400 0 97 497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008515
X-RAY DIFFRACTIONf_angle_d1.375801
X-RAY DIFFRACTIONf_dihedral_angle_d9.604264
X-RAY DIFFRACTIONf_chiral_restr0.053110
X-RAY DIFFRACTIONf_plane_restr0.01422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2505-1.3470.2991460.23112392X-RAY DIFFRACTION94
1.347-1.48260.19191410.17192576X-RAY DIFFRACTION100
1.4826-1.69710.19661200.14582583X-RAY DIFFRACTION99
1.6971-2.13820.17441190.16122625X-RAY DIFFRACTION100
2.1382-52.33580.17271410.19152720X-RAY DIFFRACTION99

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