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- PDB-435d: 5'-R(*UP*AP*GP*CP*CP*CP*C)-3', 5'-R(*GP*GP*GP*GP*CP*UP*A)-3' -

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Basic information

Entry
Database: PDB / ID: 435d
Title5'-R(*UP*AP*GP*CP*CP*CP*C)-3', 5'-R(*GP*GP*GP*GP*CP*UP*A)-3'
Components
  • RNA (5'-R(*GP*GP*GP*GP*CP*UP*A)-3')
  • RNA (5'-R(*UP*AP*GP*CP*CP*CP*C)-3')
KeywordsRNA / 7 BASE-PAIR TRNA ALA ACCEPTOR STEM C70 MUTANT / DOUBLE HELIX
Function / homologyRNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMueller, U. / Schuebel, H. / Sprinzl, M. / Heinemann, U.
CitationJournal: RNA / Year: 1999
Title: Crystal structure of acceptor stem of tRNA(Ala) from Escherichia coli shows unique G.U wobble base pair at 1.16 A resolution.
Authors: Mueller, U. / Schubel, H. / Sprinzl, M. / Heinemann, U.
History
DepositionOct 23, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Jun 14, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_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_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(*UP*AP*GP*CP*CP*CP*C)-3')
B: RNA (5'-R(*GP*GP*GP*GP*CP*UP*A)-3')
C: RNA (5'-R(*UP*AP*GP*CP*CP*CP*C)-3')
D: RNA (5'-R(*GP*GP*GP*GP*CP*UP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9126
Polymers8,8664
Non-polymers462
Water2,396133
1
A: RNA (5'-R(*UP*AP*GP*CP*CP*CP*C)-3')
B: RNA (5'-R(*GP*GP*GP*GP*CP*UP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,4563
Polymers4,4332
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA (5'-R(*UP*AP*GP*CP*CP*CP*C)-3')
D: RNA (5'-R(*GP*GP*GP*GP*CP*UP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,4563
Polymers4,4332
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.680, 26.697, 30.459
Angle α, β, γ (deg.)104.29, 104.22, 91.66
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

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Components

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


Mass: 2156.347 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: RNA chain RNA (5'-R(*GP*GP*GP*GP*CP*UP*A)-3')


Mass: 2276.419 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.54 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1SPERMINE11
2KCL11
3MPD11
4MPD12
Crystal grow
*PLUS
Temperature: 21 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mMsodium cacodylate1drop
212 mMspermine tetra-HCl1drop
3100 mM1dropKCl
410 %(v/v)1drop
50.5 mMRNA1drop
635 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 28, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.4→15 Å / Num. all: 13834 / Num. obs: 13834 / % possible obs: 88.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Rmerge(I) obs: 0.057
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.288 / % possible all: 80.7
Reflection
*PLUS
% possible obs: 89.5 %
Reflection shell
*PLUS
% possible obs: 80.7 % / Mean I/σ(I) obs: 2.3

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CANONICAL A-FORM RNA DUPLEX

Resolution: 1.4→15 Å / Num. parameters: 6493 / Num. restraintsaints: 20551 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: PARKINSON, G. ET AL.
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 627 4.6 %THIN SHELL
Rwork0.1587 ---
all0.1609 13695 --
obs--88.7 %-
Solvent computationSolvent model: MOEWS & KRETSINGER,J.MOL.BIOL.91(1973)201-228
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 721
Refinement stepCycle: LAST / Resolution: 1.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 586 2 133 721
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.028
X-RAY DIFFRACTIONs_angle_d0.01
X-RAY DIFFRACTIONs_similar_dist0.034
X-RAY DIFFRACTIONs_from_restr_planes0.021
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.009
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.004
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.025
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.018
X-RAY DIFFRACTIONs_approx_iso_adps0.043
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.218 / Rfactor Rwork: 0.158
Solvent computation
*PLUS
Displacement parameters
*PLUS

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