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- PDB-248d: CRYSTAL STRUCTURES OF AN A-FORM DUPLEX WITH SINGLE-ADENOSINE BULG... -

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Basic information

Entry
Database: PDB / ID: 248d
TitleCRYSTAL STRUCTURES OF AN A-FORM DUPLEX WITH SINGLE-ADENOSINE BULGES AND A CONFORMATIONAL BASIS FOR SITE SPECIFIC RNA SELF-CLEAVAGE
ComponentsDNA/RNA (5'-R(*GP*CP*GP*)-D(*AP*TP*AP*TP*AP*)-R(*CP*GP*C)-3'), ORTHORHOMBIC
KeywordsDNA/RNA / A-DNA/RNA / DOUBLE HELIX / BULGES / DNA-RNA complex
Function / homologySPERMINE / DNA/RNA hybrid / DNA/RNA hybrid (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.83 Å
AuthorsPortmann, S. / Grimm, S. / Workman, C. / Usman, N. / Egli, M.
CitationJournal: Chem.Biol. / Year: 1996
Title: Crystal structures of an A-form duplex with single-adenosine bulges and a conformational basis for site-specific RNA self-cleavage.
Authors: Portmann, S. / Grimm, S. / Workman, C. / Usman, N. / Egli, M.
History
DepositionFeb 2, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: DNA/RNA (5'-R(*GP*CP*GP*)-D(*AP*TP*AP*TP*AP*)-R(*CP*GP*C)-3'), ORTHORHOMBIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8593
Polymers3,4541
Non-polymers4052
Water68538
1
A: DNA/RNA (5'-R(*GP*CP*GP*)-D(*AP*TP*AP*TP*AP*)-R(*CP*GP*C)-3'), ORTHORHOMBIC
hetero molecules

A: DNA/RNA (5'-R(*GP*CP*GP*)-D(*AP*TP*AP*TP*AP*)-R(*CP*GP*C)-3'), ORTHORHOMBIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7186
Polymers6,9082
Non-polymers8094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)25.890, 33.970, 57.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-14-

HOH

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Components

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


Mass: 3454.211 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H26N4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 1.83 Å3/Da / Density % sol: 32.86 %
Crystal growMethod: vapor diffusion / pH: 7.4 / Details: pH 7.40, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NA CACODYLATE11
3SPERMINE11
4MGCL211
5WATER12
6MPD12
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-ID
10.5 mMoligonucleotide1
210 mMsodium cacodylate1
333 mMspermine tetrahydrochloride1
42 mMmagnesium chloride1
540 %MPD1
61

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 9, 1995
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→28.78 Å / Num. all: 9641 / Num. obs: 2264 / % possible obs: 94 % / Rmerge(I) obs: 0.081
Reflection
*PLUS
% possible obs: 94 %

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Processing

Software
NameClassification
X-PLORrefinement
R-AXISdata reduction
RefinementResolution: 1.83→10 Å / σ(F): 2
RfactorNum. reflection
Rfree0.236 -
Rwork0.159 -
obs0.159 2170
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.83→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 229 28 38 295
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.28
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

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