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Basic information

Entry
Database: PDB / ID: 2h1m
TitleSynthesis, Oxidation Behavior, Crystallization and Structure of 2'-Methylseleno Guanosine Containing RNAs
Components5'-R(*GP*CP*AP*(XUG)P*AP*GP*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3'
KeywordsRNA / A-RNA STRUCTURE / MISMATCH A RNA / RIBONUCLEIC ACID / Se 2'-methylSe
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSerganov, A.A.
Citation
Journal: J.Am.Chem.Soc. / Year: 2006
Title: Synthesis, Oxidation Behavior, Crystallization and Structure of 2'-Methylseleno Guanosine Containing RNAs.
Authors: Moroder, H. / Kreutz, C. / Lang, K. / Serganov, A. / Micura, R.
#1: Journal: J.Am.Chem.Soc. / Year: 2005
Title: Syntheses of RNAs with up to 100 nucleotides containing site-specific 2'-methylseleno labels for use in X-ray crystallography.
Authors: Hobartner, C. / Rieder, R. / Kreutz, C. / Puffer, B. / Lang, K. / Polonskaia, A. / Serganov, A.A. / Micura, R.
#2: Journal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation.
Authors: Serganov, A.A. / Keiper, S. / Malinina, L. / Tereshko, V. / Skripkin, E. / Hobartner, C. / Polonskaia, A. / Phan, A.T. / Wombacher, R. / Micura, R. / Dauter, Z. / Jaschke, A. / Patel, D.J.
History
DepositionMay 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: 5'-R(*GP*CP*AP*(XUG)P*AP*GP*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3'
B: 5'-R(*GP*CP*AP*(XUG)P*AP*GP*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6865
Polymers10,3982
Non-polymers2883
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.314, 46.314, 128.348
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe biological assembly is a duplex RNA.

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Components

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


Mass: 5199.090 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4

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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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.0 M Li2SO4, 0.1 M Na-citrate pH 5.6, 0.5 M ((NH4))2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Li2SO411
2Na-citrate11
3(NH4))2SO411
4H2O11
5Li2SO412
6Na-citrate12
7H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.978948 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 11, 2005
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978948 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 2227 / Num. obs: 2227 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.112 / Net I/σ(I): 12.7
Reflection shellResolution: 2.9→3 Å / Mean I/σ(I) obs: 6.5 / Num. unique all: 221 / Rsym value: 0.32 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CBASSdata collection
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Similar RNA structure from the crystal grown in different conditions.

Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.949 / SU B: 42.148 / SU ML: 0.323 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2386 102 4.6 %RANDOM
Rwork0.21225 ---
all0.21352 2227 --
obs0.21352 2118 97.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.247 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20.43 Å20 Å2
2--0.86 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 680 15 0 695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.021772
X-RAY DIFFRACTIONr_angle_refined_deg1.12531198
X-RAY DIFFRACTIONr_chiral_restr0.0470.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.02332
X-RAY DIFFRACTIONr_nbd_refined0.1540.2292
X-RAY DIFFRACTIONr_nbtor_refined0.2690.2496
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.29
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1080.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0810.22
X-RAY DIFFRACTIONr_scbond_it0.47131088
X-RAY DIFFRACTIONr_scangle_it0.9224.51198
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 6 -
Rwork0.343 170 -
obs--99.44 %
Refinement TLS params.Method: refined / Origin x: -17.4451 Å / Origin y: 30.2251 Å / Origin z: 0.2219 Å
111213212223313233
T0.3097 Å20.1043 Å20.0045 Å2-0.1852 Å2-0.0046 Å2--0.1447 Å2
L0.3148 °20.223 °2-0.1367 °2-0.1581 °2-0.1174 °2--6.3136 °2
S0.0344 Å °0.0583 Å °0.038 Å °0.1622 Å °-0.0879 Å °-0.0038 Å °0.7874 Å °0.4599 Å °0.0534 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 161 - 16
2X-RAY DIFFRACTION1BB17 - 321 - 16
3X-RAY DIFFRACTION1AC - E17 - 181

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