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- PDB-2r21: Structure of the RNA brominated tridecamer r(GCGUU-5BUGAAACGC) at... -

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Basic information

Entry
Database: PDB / ID: 2r21
TitleStructure of the RNA brominated tridecamer r(GCGUU-5BUGAAACGC) at 1.6 A (BrMn)
ComponentsRNA (5'-R(*GP*CP*GP*UP*UP*(5BU)P*GP*AP*AP*AP*CP*GP*C)-3')
KeywordsRNA / manganese / asymmetry / elecrostatic / mnovalent
Function / homology: / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.59 Å
AuthorsTimsit, Y. / Bombard, S.
CitationJournal: TO BE PUBLISHED
Title: 1.3 A resolution 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 / struct_conn_type
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

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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)8,6207
Polymers8,4732
Non-polymers1475
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.250, 25.650, 29.720
Angle α, β, γ (deg.)98.13, 106.15, 100.83
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.: 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.: 162 / 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: 2.1 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.5mM MnCl2, 100mM NaCl, 30% MPD, 50mM Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
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: 0.919487,0.919704,0.88558,0.979776
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 4, 2003
RadiationMonochromator: Si (111) crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9194871
20.9197041
30.885581
40.9797761
ReflectionResolution: 1.59→20 Å / Num. all: 8713 / Num. obs: 8713 / % possible obs: 94.4 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.117 / Rsym value: 9.4 / Net I/σ(I): 4.8
Reflection shellResolution: 1.59→1.68 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1160 / Rsym value: 21 / % possible all: 84.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
CNSphasing
CNSrefinement
PDB_EXTRACT3data extraction
MAR345dtbdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.59→20 Å / σ(F): 146
RfactorNum. reflection% reflection
Rfree0.191 1376 5.1 %
Rwork0.169 --
obs-8713 56 %
Solvent computationBsol: 55.742 Å2
Displacement parametersBiso mean: 14.009 Å2
Baniso -1Baniso -2Baniso -3
1--0.299 Å2-0.023 Å2-0.901 Å2
2--0.339 Å2-0.669 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.59→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 552 5 162 719
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.89251
X-RAY DIFFRACTIONc_bond_d0.005185
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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