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- PDB-1qbp: CRYSTAL STRUCTURE OF A BROMINATED RNA HELIX WITH FOUR MISMATCHED ... -

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Basic information

Entry
Database: PDB / ID: 1qbp
TitleCRYSTAL STRUCTURE OF A BROMINATED RNA HELIX WITH FOUR MISMATCHED BASE PAIRS
Components5'-R(*UP*GP*(CBV)P*(CBV)P*AP*GP*UP*UP*CP*GP*CP*UP*GP*GP*C)-3'
KeywordsRNA / BROMINATED CYTOSINE / MISMATCHED BASE PAIRS
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsAnderson, A.C. / O'Neil, R.H. / Filman, D.J. / Frederick, C.A.
CitationJournal: Biochemistry / Year: 1999
Title: Crystal structure of a brominated RNA helix with four mismatched base pairs: An investigation into RNA conformational variability.
Authors: Anderson, A.C. / O'Neil, R.H. / Filman, D.J. / Frederick, C.A.
History
DepositionApr 26, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*UP*GP*(CBV)P*(CBV)P*AP*GP*UP*UP*CP*GP*CP*UP*GP*GP*C)-3'
B: 5'-R(*UP*GP*(CBV)P*(CBV)P*AP*GP*UP*UP*CP*GP*CP*UP*GP*GP*C)-3'
C: 5'-R(*UP*GP*(CBV)P*(CBV)P*AP*GP*UP*UP*CP*GP*CP*UP*GP*GP*C)-3'
D: 5'-R(*UP*GP*(CBV)P*(CBV)P*AP*GP*UP*UP*CP*GP*CP*UP*GP*GP*C)-3'
E: 5'-R(*UP*GP*(CBV)P*(CBV)P*AP*GP*UP*UP*CP*GP*CP*UP*GP*GP*C)-3'
F: 5'-R(*UP*GP*(CBV)P*(CBV)P*AP*GP*UP*UP*CP*GP*CP*UP*GP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)29,5126
Polymers29,5126
Non-polymers00
Water1,982110
1
A: 5'-R(*UP*GP*(CBV)P*(CBV)P*AP*GP*UP*UP*CP*GP*CP*UP*GP*GP*C)-3'
B: 5'-R(*UP*GP*(CBV)P*(CBV)P*AP*GP*UP*UP*CP*GP*CP*UP*GP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)9,8372
Polymers9,8372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-R(*UP*GP*(CBV)P*(CBV)P*AP*GP*UP*UP*CP*GP*CP*UP*GP*GP*C)-3'
D: 5'-R(*UP*GP*(CBV)P*(CBV)P*AP*GP*UP*UP*CP*GP*CP*UP*GP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)9,8372
Polymers9,8372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 5'-R(*UP*GP*(CBV)P*(CBV)P*AP*GP*UP*UP*CP*GP*CP*UP*GP*GP*C)-3'
F: 5'-R(*UP*GP*(CBV)P*(CBV)P*AP*GP*UP*UP*CP*GP*CP*UP*GP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)9,8372
Polymers9,8372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.450, 24.270, 104.450
Angle α, β, γ (deg.)90.00, 118.76, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

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


Mass: 4918.642 Da / Num. of mol.: 6 / Source method: obtained synthetically
Details: SYNTHESIZED BY THE SOLID-PHASE PHOSPHORAMIDITE METHOD
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.03 Å3/Da / Density % sol: 39.45 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25 MM SODIUM CACODYLATE, 45 MM MGCL2, 60 MM SPERMINE, 6.7 % MPD, RESERVOIR 40 % MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2MGCL211
3SPERMINE11
4MPD11
5MPD12
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.5 mMRNA1drop
225 mMsodium cacodylate1drop
340-50 mM1dropMgCl2
460 mMspermine1drop
56.7 %1drop
640 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.92036
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Feb 25, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92036 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 11984 / Num. obs: 11919 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
MLPHAREphasing
X-PLOR3.851refinement
CCP4(TRUNCATE)data scaling
RefinementResolution: 2.1→999 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.253 1192 -
Rwork0.217 --
obs0.217 11919 97 %
all-12344 -
Refinement stepCycle: LAST / Resolution: 2.1→999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1800 12 110 1922
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d1.21
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
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
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 9999 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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