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- PDB-1g2j: RNA OCTAMER R(CCCP*GGGG) CONTAINING PHENYL RIBONUCLEOTIDE -

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Basic information

Entry
Database: PDB / ID: 1g2j
TitleRNA OCTAMER R(CCCP*GGGG) CONTAINING PHENYL RIBONUCLEOTIDE
Components5'-R(*CP*CP*CP*(PYY)P*GP*GP*GP*G)-3'
KeywordsRNA / RNA duplex / phenyl-ribonucleotide
Function / homologyRNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsMinasov, G. / Matulic-Adamic, J. / Wilds, C.J. / Haeberli, P. / Usman, N. / Beigelman, L. / Egli, M.
CitationJournal: RNA / Year: 2000
Title: Crystal structure of an RNA duplex containing phenyl-ribonucleotides, hydrophobic isosteres of the natural pyrimidines.
Authors: Minasov, G. / Matulic-Adamic, J. / Wilds, C.J. / Haeberli, P. / Usman, N. / Beigelman, L. / Egli, M.
History
DepositionOct 20, 2000Deposition site: NDB / Processing site: NDB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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_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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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
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(*CP*CP*CP*(PYY)P*GP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,6043
Polymers2,5241
Non-polymers802
Water66737
1
A: 5'-R(*CP*CP*CP*(PYY)P*GP*GP*GP*G)-3'
hetero molecules

A: 5'-R(*CP*CP*CP*(PYY)P*GP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2086
Polymers5,0472
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Unit cell
Length a, b, c (Å)24.310, 24.310, 123.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-14-

CA

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Components

#1: RNA chain 5'-R(*CP*CP*CP*(PYY)P*GP*GP*GP*G)-3'


Mass: 2523.602 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.09 Å3/Da / Density % sol: 41.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Oligonucleotide, Calcium Acetate, Sodium Cacodylate, PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1Oligonucleotide11
2Calcium Acetate11
3Sodium Cacodylate11
4PEG 800011
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.5 mMRNA1drop
250 mMcalcium acetate1drop
325 mMsodium cacodylate1drop
44.5 %(v/v)PEG80001drop
50.2 Mcalcium acetate1reservoir
60.1 Msodium cacodylate1reservoir
718 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→20 Å / Num. all: 1904 / Num. obs: 1904 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.6 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 20.5
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 17.3 / Num. unique all: 186 / % possible all: 99.5
Reflection
*PLUS
Num. measured all: 25862
Reflection shell
*PLUS
% possible obs: 99.5 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RNA tetramer duplex

Resolution: 1.97→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Stereochemistry target values: G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman, Acta Cryst. D, 52, 57-64 (1996).
Details: Used residual target
RfactorNum. reflection% reflectionSelection details
Rfree0.269 185 -random
Rwork0.217 ---
all-1736 --
obs-1736 95.3 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--17.632 Å2-3.89 Å20 Å2
2---17.632 Å20 Å2
3---35.264 Å2
Refinement stepCycle: LAST / Resolution: 1.97→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 167 2 45 214
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d29.47
X-RAY DIFFRACTIONc_improper_angle_d1.94
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg29.47
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.94

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