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- PDB-420d: CRYSTAL STRUCTURE OF A 16-MER RNA DUPLEX WITH NON-ADJACENT A(ANTI... -

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Basic information

Entry
Database: PDB / ID: 420d
TitleCRYSTAL STRUCTURE OF A 16-MER RNA DUPLEX WITH NON-ADJACENT A(ANTI).G(SYN) MISMATCHES
ComponentsRNA (5'-R(*GP*CP*AP*GP*AP*GP*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3')
KeywordsRNA / A-RNA STRUCTURE / MISMATCH A RNA
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsPan, B. / Mitra, S.N. / Sundaralingam, M.
CitationJournal: Biochemistry / Year: 1999
Title: Crystal structure of an RNA 16-mer duplex R(GCAGAGUUAAAUCUGC)2 with nonadjacent G(syn).A+(anti) mispairs.
Authors: Pan, B. / Mitra, S.N. / Sundaralingam, M.
History
DepositionAug 13, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*GP*CP*AP*GP*AP*GP*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3')
B: RNA (5'-R(*GP*CP*AP*GP*AP*GP*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2673
Polymers10,2442
Non-polymers231
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.530, 42.530, 128.060
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
11A-89-

NA

21A-73-

HOH

31B-72-

HOH

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Components

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


Mass: 5122.103 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growMethod: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2KCL11
3CACL211
4NA HEPES11
5PEG 40011
6WATER12
7PEG 40012
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mMRNA1drop
250 mMsodium HEPES1drop
350 mM1dropKCl
45 mM1dropCaCl2
55 %PEG4001drop
630 %PEG4001reservoir
71

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 27, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.82→21.27 Å / Num. obs: 7377 / % possible obs: 87 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.073
Reflection
*PLUS
Highest resolution: 1.82 Å / Lowest resolution: 21.27 Å / Num. obs: 5521 / % possible obs: 81 % / Observed criterion σ(F): 2 / Redundancy: 2.8 %
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.99 Å / % possible obs: 52.5 %

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
R-AXISIIC V. 2.1data reduction
MSCdata scaling
RefinementResolution: 1.9→8 Å / Isotropic thermal model: ISOTROPIC / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.296 569 10 %
Rwork0.197 --
all0.207 5433 -
obs0.197 5433 80.8 %
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 678 1 56 735
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
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_deg0.9
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: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg12.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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