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- PDB-485d: A SULFATE POCKET FORMED BY THREE GOU PAIRS IN THE STRUCTURE OF A ... -

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Basic information

Entry
Database: PDB / ID: 485d
TitleA SULFATE POCKET FORMED BY THREE GOU PAIRS IN THE STRUCTURE OF A NONAMERIC RNA
ComponentsRNA/DNA(5'-R(*CP*GP*UP*GP*AP*UP*CP*GP)-D(*C)-3')
KeywordsDNA-RNA HYBRID / RNA / DNA/RNA HYBRID / SULFATE ION / DNA-RNA HYBRID complex
Function / homologyDNA/RNA hybrid
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 Å
AuthorsMasquida, B. / Sauter, C. / Westhof, E.
CitationJournal: RNA / Year: 1999
Title: A sulfate pocket formed by three GoU pairs in the 0.97 A resolution X-ray structure of a nonameric RNA.
Authors: Masquida, B. / Sauter, C. / Westhof, E.
History
DepositionAug 13, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_keywords / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_keywords.text / _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/DNA(5'-R(*CP*GP*UP*GP*AP*UP*CP*GP)-D(*C)-3')
B: RNA/DNA(5'-R(*CP*GP*UP*GP*AP*UP*CP*GP)-D(*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,7283
Polymers5,6312
Non-polymers961
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.958, 39.958, 67.445
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Cell settingtrigonal
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-19-

SO4

21A-101-

HOH

31A-123-

HOH

41A-133-

HOH

51A-153-

HOH

61B-102-

HOH

71B-104-

HOH

81B-107-

HOH

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Components

#1: DNA/RNA hybrid RNA/DNA(5'-R(*CP*GP*UP*GP*AP*UP*CP*GP)-D(*C)-3')


Mass: 2815.743 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 1.84 Å3/Da / Density % sol: 33.15 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2.2-2.6 M AMMONIUM SULFATE, 5-50 MM MAGNESIUM SULFATE, 50 MM SODIUM CACODYLATE, 1MM SPERMINE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 310K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2MGSO411
3SODIUM CACODYLATE,11
4SPERMINE11
5(NH4)2SO412
6MGSO412
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlRNA1drop
25 mM1dropMgCl2
310 mMsodium cacodylate1drop
42.2-2.6 Mammonium sulfate1reservoir
550 mMsodium cacodylate1reservoir
61 mMspermine1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9343
DetectorDetector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9343 Å / Relative weight: 1
ReflectionResolution: 0.97→20 Å / Num. all: 23838 / Num. obs: 23838 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.91 % / Rmerge(I) obs: 0.041
Reflection shellResolution: 0.97→0.99 Å / Redundancy: 2.63 % / Rmerge(I) obs: 0.446 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 140902
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.97→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1954 1292 5 %THIN SHELLS
Rwork0.1487 ---
all0.1503 23838 --
obs0.1503 23838 99.8 %-
Refinement stepCycle: LAST / Resolution: 0.97→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 342 5 84 431
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.018
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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