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- PDB-2r1s: Structure of the RNA brominated tridecamer r(GCGUU-5BUGAAACGC) at... -

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Basic information

Entry
Database: PDB / ID: 2r1s
TitleStructure of the RNA brominated tridecamer r(GCGUU-5BUGAAACGC) at 1.4 A (Br1)
ComponentsRNA (5'-R(*GP*CP*GP*UP*UP*(5BU)P*GP*AP*AP*AP*CP*GP*C)-3')
KeywordsRNA / asymmetry / electrostatic / monovalent cations / structural plasticity
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsTimsit, Y. / Bombard, S.
CitationJournal: Rna / Year: 2007
Title: The 1.3 A resolution structure of the RNA tridecamer r(GCGUUUGAAACGC): Metal ion binding correlates with base unstacking and groove contraction.
Authors: Timsit, Y. / Bombard, S.
History
DepositionAug 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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_conn_type / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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*GP*UP*UP*(5BU)P*GP*AP*AP*AP*CP*GP*C)-3')
B: RNA (5'-R(*GP*CP*GP*UP*UP*(5BU)P*GP*AP*AP*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6128
Polymers8,4732
Non-polymers1396
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.380, 25.670, 29.920
Angle α, β, γ (deg.)98.64, 105.43, 100.67
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 4236.421 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 30% MPD, 100mM NaCl, 50 mM Tris, 3mM MnCl2, 2mM MgCl2, 0.5 mM RNA, pH 7.0, VAPOR DIFFUSION, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2NaCl11
3Tris11
4MnCl211
5MgCl211
6MPD12
7NaCl12
8Tris12
9MnCl212
10MgCl212

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.919487 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 3, 2003
RadiationMonochromator: Si (111) crystals / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919487 Å / Relative weight: 1
ReflectionResolution: 1.4→14.1 Å / Num. obs: 12174 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.035 / Rsym value: 2.3 / Net I/σ(I): 19.4
Reflection shellResolution: 1.4→1.49 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 8.8 / Num. unique all: 1310 / Rsym value: 8 / % possible all: 67.2

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
PDB_EXTRACT3data extraction
MAR345dtbdata collection
CNSphasing
RefinementResolution: 1.4→14.1 Å / σ(F): 209 / Stereochemistry target values: mlf
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1971 7.2 %random
Rwork0.159 ---
obs0.159 12174 80.1 %-
Solvent computationBsol: 47.016 Å2
Displacement parametersBiso mean: 11.026 Å2
Baniso -1Baniso -2Baniso -3
1--0.055 Å2-0.381 Å2-0.478 Å2
2---0.068 Å20.104 Å2
3---0.122 Å2
Refinement stepCycle: LAST / Resolution: 1.4→14.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 552 6 176 734
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.89206
X-RAY DIFFRACTIONc_bond_d0.003882
X-RAY DIFFRACTIONc_dihedral_angle_d10.3
X-RAY DIFFRACTIONo_improper_angle_d1.2537
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1dna-rna_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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