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- PDB-333d: THE CRYSTAL STRUCTURE OF AN RNA OLIGOMER INCORPORATING TANDEM ADE... -

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Basic information

Entry
Database: PDB / ID: 333d
TitleTHE CRYSTAL STRUCTURE OF AN RNA OLIGOMER INCORPORATING TANDEM ADENOSINE-INOSINE MISMATCHES
ComponentsRNA (5'-R(*CP*GP*CP*AP*IP*GP*CP*G)-3')
KeywordsRNA / A-RNA / DOUBLE HELIX / INTERNAL LOOP / MISMATCHED
Function / homologyRNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsCarter, R.J. / Baeyens, K.J. / SantaLucia Jr., J. / Turner, D.H. / Holbrook, S.R.
CitationJournal: Nucleic Acids Res. / Year: 1997
Title: The crystal structure of an RNA oligomer incorporating tandem adenosine-inosine mismatches.
Authors: Carter, R.J. / Baeyens, K.J. / SantaLucia, J. / Turner, D.H. / Holbrook, S.R.
History
DepositionMay 20, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Oct 16, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 21, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*CP*GP*CP*AP*IP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,6062
Polymers2,5661
Non-polymers401
Water1086
1
A: RNA (5'-R(*CP*GP*CP*AP*IP*GP*CP*G)-3')
hetero molecules

A: RNA (5'-R(*CP*GP*CP*AP*IP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2114
Polymers5,1312
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Unit cell
Length a, b, c (Å)39.050, 39.050, 58.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-14-

HOH

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Components

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


Mass: 2565.602 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.52 Å3/Da / Density % sol: 49.7 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5 / Details: pH 7.50, VAPOR DIFFUSION, HANGING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 40011
3CACL211
4HEPES11
5WATER12
6PEG 40012
7CACL212
8HEPES12
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.5 mMprotein1drop
20.2 M1reservoirCaCl2
30.1 MHEPES1reservoirpH7.5
428 %PEG4001reservoir
51
61
71
81

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 21, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.52→12 Å / Num. all: 5952 / Num. obs: 1014 / % possible obs: 91.8 % / Observed criterion σ(I): 3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.079
Reflection
*PLUS
Highest resolution: 2.52 Å / Lowest resolution: 25 Å / % possible obs: 91.8 % / Observed criterion σ(I): 3 / Redundancy: 5.9 % / Num. measured all: 5952

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
R-AXISdata reduction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CGC:GCG FRAGMENT OF ARL048

Resolution: 2.52→12 Å / σ(F): 3
Details: NUCLEIC ACID RNA-DNA PARAMETER FILE: G. PARKINSON,ET AL. (1996) ACTA CRYST. D52, 57-64
RfactorNum. reflection% reflection
Rfree0.266 -10 %
Rwork0.246 --
obs0.246 1014 -
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.52→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 170 1 6 177
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d11
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.39
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
Xplor fileSerial no: 1 / Param file: TOPOL_BERMAN.RNA / Topol file: PARAM_BERMAN.RNA
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.52 Å / Lowest resolution: 12 Å / σ(F): 3 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg11
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.39

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