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- PDB-2r20: Structure of the RNA brominated tridecamer r(GCGUU-5BUGAAACGC) at... -

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Basic information

Entry
Database: PDB / ID: 2r20
TitleStructure of the RNA brominated tridecamer r(GCGUU-5BUGAAACGC) at 1.3 A (Br2)
ComponentsRNA (5'-R(*GP*CP*GP*UP*UP*(5BU)P*GP*AP*AP*AP*CP*GP*C)-3')
KeywordsRNA / asymmetry / metal ion binding / unstacking / electrostatic
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 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 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 / 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
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.280, 25.800, 29.990
Angle α, β, γ (deg.)98.620, 105.580, 100.920
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.: 165 / 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: 2.13 Å3/Da / Density % sol: 42.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5 mM MgCl2, 5 mM MnCl2, 100 mM NaCl, 30 % MPD, 50 mM tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2NaCl11
3tris11
4MgCl211
5MnCl211
6MPD12
7NaCl12
8tris12
9MgCl212
10MnCl212

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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, 2002 / Details: mirrors
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: 1.3→20 Å / Num. all: 13060 / Num. obs: 13060 / % possible obs: 91 % / Rsym value: 4.9 / Net I/σ(I): 9.1
Reflection shellResolution: 1.3→1.45 Å / Mean I/σ(I) obs: 8.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
CNSrefinement
PDB_EXTRACT3data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MAD / Resolution: 1.3→20 Å / σ(F): 111
RfactorNum. reflection% reflectionSelection details
Rfree0.195 2355 6.8 %random
Rwork0.181 ---
obs-13060 73.7 %-
Solvent computationBsol: 60.67 Å2
Displacement parametersBiso mean: 13.936 Å2
Baniso -1Baniso -2Baniso -3
1--0.443 Å2-0.812 Å2-1.108 Å2
2--0.006 Å20.514 Å2
3---0.437 Å2
Refinement stepCycle: LAST / Resolution: 1.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 552 6 165 723
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.0831.5
X-RAY DIFFRACTIONc_mcangle_it1.3732
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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