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- PDB-283d: A CURVED RNA HELIX INCORPORATING AN INTERNAL LOOP WITH G-A AND A-... -

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Basic information

Entry
Database: PDB / ID: 283d
TitleA CURVED RNA HELIX INCORPORATING AN INTERNAL LOOP WITH G-A AND A-A NON-WATSON-CRICK BASE PAIRING
ComponentsRNA (5'-R(*GP*GP*CP*CP*GP*AP*AP*AP*GP*GP*CP*C)-3')
KeywordsRNA / UNUSUAL RNA / DOUBLE HELIX / CURVED / INTERNAL LOOP / MISMATCHED
Function / homology: / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBaeyens, K.J. / De Bondt, H.L. / Pardi, A. / Holbrook, S.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: A curved RNA helix incorporating an internal loop with G.A and A.A non-Watson-Crick base pairing.
Authors: Baeyens, K.J. / De Bondt, H.L. / Pardi, A. / Holbrook, S.R.
History
DepositionSep 3, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Sep 30, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 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(*GP*GP*CP*CP*GP*AP*AP*AP*GP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9442
Polymers3,8891
Non-polymers551
Water32418
1
A: RNA (5'-R(*GP*GP*CP*CP*GP*AP*AP*AP*GP*GP*CP*C)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)7,8894
Polymers7,7792
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+5/61
Unit cell
Length a, b, c (Å)37.710, 37.710, 88.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 3889.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Description: THE DODECAMER WAS PREPARED BY TRANSCRIPTION WITH T7 RNA POLYMERASE FROM A SINGLE STRANDED DNA TEMPLATE.
Plasmid: PAR1219 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.33 Å3/Da / Density % sol: 51.2 %
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
3NACLSodium chloride11
4MNCL211
5BIS-TRIS-PROPANE_HCL11
Crystal
*PLUS
Density % sol: 51.2 %
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mMRNA1drop
220 mM1reservoirNaCl
35 mM1reservoirMnCl2
450 mMTris-HCl1reservoir
530 %PEG4001reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 10, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 1811 / % possible obs: 94.3 % / Observed criterion σ(I): 0 / Redundancy: 2.85 % / Rmerge(I) obs: 0.0745 / Net I/σ(I): 2.8
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 25 Å / Num. obs: 1869 / % possible obs: 92.4 % / Observed criterion σ(I): 0 / Redundancy: 2.85 %

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Processing

Software
NameClassification
X-PLORrefinement
R-AXISdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STANDARD A-FORM DUPLEX AND ARL048

Resolution: 2.3→8 Å / Num. restraintsaints: 22 / Cross valid method: FREE-R / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.198 138 10 %RANDOM
Rwork0.186 ---
obs0.186 1502 --
Displacement parametersBiso mean: 23.64 Å2
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 258 1 18 277
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
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_deg1.15
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_it1.3
X-RAY DIFFRACTIONx_mcangle_it1.7
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 8 Å / σ(F): 3 / % reflection Rfree: 10 % / Rfactor Rfree: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.1

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