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- PDB-2r22: Structure of the native RNA tridecamer r(GCGUUUGAAACGC) at 1.5 A ... -

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Basic information

Entry
Database: PDB / ID: 2r22
TitleStructure of the native RNA tridecamer r(GCGUUUGAAACGC) at 1.5 A (NatMn)
ComponentsRNA (5'-R(*GP*CP*GP*UP*UP*UP*GP*AP*AP*AP*CP*GP*C)-3')
KeywordsRNA / monovalent / electrostatic / asymmetry / manganese
Function / homology: / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsTimsit, Y. / Bombard, S.
CitationJournal: TO BE PUBLISHED
Title: The 1.3 A structure of the tridecamer r(GCGUUUGAAACGC)
Authors: Timsit, Y. / Bombard, S.
History
DepositionAug 24, 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
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.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.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

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


Theoretical massNumber of molelcules
Total (without water)8,4627
Polymers8,3152
Non-polymers1475
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.280, 25.500, 29.600
Angle α, β, γ (deg.)97.97, 106.69, 101.62
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 4157.525 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: 3 mM MnCl2, 100 mM NaCl, 50 mM Tris, 30 % MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2NaCl11
3Tris11
4MnCl211
5MPD12
6NaCl12
7Tris12
8MnCl212

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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 / Details: mirrors
RadiationMonochromator: Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919487 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. all: 12814 / Num. obs: 12814 / % possible obs: 88.7 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.09 / Rsym value: 6.4 / Net I/σ(I): 7.8
Reflection shellResolution: 1.4→1.53 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1838 / Rsym value: 19.7 / % possible all: 92

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3data extraction
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementResolution: 1.4→20 Å / σ(F): 104
RfactorNum. reflection% reflection
Rfree0.2 1457 5.5 %
Rwork0.178 --
obs-12814 63.3 %
Solvent computationBsol: 40.159 Å2
Displacement parametersBiso mean: 13.727 Å2
Baniso -1Baniso -2Baniso -3
1--4.257 Å2-1.789 Å2-2.954 Å2
2--3.193 Å20.929 Å2
3---1.064 Å2
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 550 5 145 700
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.89166
X-RAY DIFFRACTIONc_bond_d0.003646
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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