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- PDB-1j9h: Crystal Structure of an RNA Duplex with Uridine Bulges -

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Basic information

Entry
Database: PDB / ID: 1j9h
TitleCrystal Structure of an RNA Duplex with Uridine Bulges
Components5'-R(*GP*UP*GP*UP*CP*GP*(CBR)P*AP*C)-3'
KeywordsRNA / Uridine Bulge / RNA duplex / A-form / Kink / Metal binding
Function / homologyRNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsXiong, Y. / Deng, J. / Sudarsanakumar, C. / Sundaralingam, M.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of an RNA duplex r(gugucgcac)(2) with uridine bulges.
Authors: Xiong, Y. / Deng, J. / Sudarsanakumar, C. / Sundaralingam, M.
History
DepositionMay 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2001Provider: 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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_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: 5'-R(*GP*UP*GP*UP*CP*GP*(CBR)P*AP*C)-3'
B: 5'-R(*GP*UP*GP*UP*CP*GP*(CBR)P*AP*C)-3'
C: 5'-R(*GP*UP*GP*UP*CP*GP*(CBR)P*AP*C)-3'
D: 5'-R(*GP*UP*GP*UP*CP*GP*(CBR)P*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8038
Polymers11,6434
Non-polymers1604
Water2,630146
1
A: 5'-R(*GP*UP*GP*UP*CP*GP*(CBR)P*AP*C)-3'
B: 5'-R(*GP*UP*GP*UP*CP*GP*(CBR)P*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9014
Polymers5,8212
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-R(*GP*UP*GP*UP*CP*GP*(CBR)P*AP*C)-3'
D: 5'-R(*GP*UP*GP*UP*CP*GP*(CBR)P*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9014
Polymers5,8212
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.180, 47.180, 80.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

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


Mass: 2910.639 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 1.96 Å3/Da / Density % sol: 37.09 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: 20mM sodium cacodylate (pH 6.0), 10mM calcium chloride, 100mM sodium chloride, and 10%(v/v) MPD against 50% MPD in the reservoir, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2CaCl211
3NaCl11
4MPD11
5MPD12
Crystal grow
*PLUS
Temperature: 293 K
Components of the solutions
*PLUS
IDConc.Crystal-IDSol-IDChemical formula
120 mM1drop
210 mM1dropCaCl2
3100 mM1dropNaCl
410 %(v/v)1drop
550 %1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. obs: 33934 / % possible obs: 99.3 % / Redundancy: 9 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 22
Reflection
*PLUS
Lowest resolution: 20 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
MLPHAREphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.4→20 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.234 3228 -
Rwork0.212 --
obs-33271 97.8 %
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 748 10 146 904
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 20 Å / σ(F): 2 / Rfactor obs: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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