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- PDB-2g3s: RNA structure containing GU base pairs -

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Basic information

Entry
Database: PDB / ID: 2g3s
TitleRNA structure containing GU base pairs
Components5'-R(*GP*GP*CP*GP*UP*GP*CP*C)-3'
KeywordsRNA / RNA crystal structure / tandem GU base pairs
Function / homologyRNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 Å
AuthorsJang, S.B. / Hung, L.W. / Jeong, M.S. / Holbrook, E.L. / Chen, X. / Turner, D.H. / Holbrook, S.R.
CitationJournal: Biophys.J. / Year: 2006
Title: The crystal structure at 1.5 angstroms resolution of an RNA octamer duplex containing tandem G.U basepairs
Authors: Jang, S.B. / Hung, L.W. / Jeong, M.S. / Holbrook, E.L. / Chen, X. / Turner, D.H. / Holbrook, S.R.
History
DepositionFeb 20, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / pdbx_entity_src_syn / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name / _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.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 / _struct_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: 5'-R(*GP*GP*CP*GP*UP*GP*CP*C)-3'
B: 5'-R(*GP*GP*CP*GP*UP*GP*CP*C)-3'
C: 5'-R(*GP*GP*CP*GP*UP*GP*CP*C)-3'
D: 5'-R(*GP*GP*CP*GP*UP*GP*CP*C)-3'
E: 5'-R(*GP*GP*CP*GP*UP*GP*CP*C)-3'
F: 5'-R(*GP*GP*CP*GP*UP*GP*CP*C)-3'
G: 5'-R(*GP*GP*CP*GP*UP*GP*CP*C)-3'
H: 5'-R(*GP*GP*CP*GP*UP*GP*CP*C)-3'
I: 5'-R(*GP*GP*CP*GP*UP*GP*CP*C)-3'
J: 5'-R(*GP*GP*CP*GP*UP*GP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,62412
Polymers25,57610
Non-polymers492
Water11,043613
1
A: 5'-R(*GP*GP*CP*GP*UP*GP*CP*C)-3'
B: 5'-R(*GP*GP*CP*GP*UP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)5,1152
Polymers5,1152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-R(*GP*GP*CP*GP*UP*GP*CP*C)-3'
D: 5'-R(*GP*GP*CP*GP*UP*GP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1393
Polymers5,1152
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 5'-R(*GP*GP*CP*GP*UP*GP*CP*C)-3'
F: 5'-R(*GP*GP*CP*GP*UP*GP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1393
Polymers5,1152
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: 5'-R(*GP*GP*CP*GP*UP*GP*CP*C)-3'
H: 5'-R(*GP*GP*CP*GP*UP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)5,1152
Polymers5,1152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: 5'-R(*GP*GP*CP*GP*UP*GP*CP*C)-3'
J: 5'-R(*GP*GP*CP*GP*UP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)5,1152
Polymers5,1152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.332, 43.998, 54.971
Angle α, β, γ (deg.)112.10, 99.03, 89.96
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 2557.577 Da / Num. of mol.: 10 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 613 / 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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M magnesium acetate, 0.1M sodium cacodylate, pH 6.5, 10% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1magnesium acetate11
2sodium cacodylate11
3MPD11
4H2O11
5magnesium acetate12
6sodium cacodylate12
7MPD12
8H2O1

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 30, 2000
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.499→19.95 Å / Num. all: 31611 / Num. obs: 30400 / % possible obs: 96.16 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.5→1.51 Å / % possible all: 91.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.499→19.95 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.285 1513 RANDOM
Rwork0.226 --
obs0.226 30400 -
all-31611 -
Refinement stepCycle: LAST / Resolution: 1.499→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1690 2 613 2305
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg0.89

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