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- PDB-4rbq: 32 base pair oligo(U) RNA -

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Basic information

Entry
Database: PDB / ID: 4rbq
Title32 base pair oligo(U) RNA
ComponentsU-Helix RNA from Trypanosome editing
KeywordsRNA / double helix / oligoU / 3' U-tail / atomic resolution / A-form RNA / Trypanosome RNA editing substrate / mitochondrion
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsMooers, B.H.M.
Citation
Journal: To be Published
Title: Structure of the Trypanosome RNA Editing U-Helix with 16 Contiguous Us
Authors: Mooers, B.H.M.
#1: Journal: Methods Mol.Biol. / Year: 2015
Title: Fusion RNAs in crystallographic studies of double-stranded RNA from trypanosome RNA editing.
Authors: Mooers, B.H.
History
DepositionSep 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 28, 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_alt_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 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: U-Helix RNA from Trypanosome editing
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4126
Polymers10,2171
Non-polymers1955
Water4,450247
1
A: U-Helix RNA from Trypanosome editing
hetero molecules

A: U-Helix RNA from Trypanosome editing
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,82512
Polymers20,4342
Non-polymers39110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z1
Buried area2920 Å2
ΔGint-29 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.890, 42.890, 266.936
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-101-

K

21A-102-

K

31A-103-

K

41A-104-

K

51A-105-

K

61A-202-

HOH

71A-205-

HOH

81A-212-

HOH

91A-216-

HOH

101A-221-

HOH

111A-225-

HOH

121A-226-

HOH

131A-319-

HOH

141A-361-

HOH

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Components

#1: RNA chain U-Helix RNA from Trypanosome editing


Mass: 10216.987 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.31 Å3/Da / Density % sol: 46.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM sodium cacodylate, pH 6.5, 200 mM potassium chloride, 75 mM magnesium acetate, 900 mM lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 10, 2009
RadiationMonochromator: side scattering I-beam bent single crystal, asymmetric cut 4.965 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.05→36.8 Å / Num. all: 45101 / Num. obs: 45101 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 9.5 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 20.1
Reflection shellHighest resolution: 1.05 Å

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
PHENIX(PHENIX.REFINE: 1.7.3_927)refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IDEAL A-FORM RNA

Resolution: 1.05→36.79 Å / SU ML: 0.1 / σ(F): 0.23 / Phase error: 16.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1537 921 2.05 %
Rwork0.1307 --
obs0.1312 44972 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.0007 Å2-0 Å20 Å2
2--1.0007 Å20 Å2
3----2.0013 Å2
Refinement stepCycle: LAST / Resolution: 1.05→36.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 675 5 247 927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004754
X-RAY DIFFRACTIONf_angle_d0.8981172
X-RAY DIFFRACTIONf_dihedral_angle_d5.895380
X-RAY DIFFRACTIONf_chiral_restr0.034159
X-RAY DIFFRACTIONf_plane_restr0.01232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.08090.261630.27766876X-RAY DIFFRACTION99
1.0809-1.11580.20981170.20166998X-RAY DIFFRACTION100
1.1158-1.15570.22511240.16436999X-RAY DIFFRACTION100
1.1557-1.2020.15751380.14476928X-RAY DIFFRACTION100
1.202-1.25670.17781640.13286994X-RAY DIFFRACTION100
1.2567-1.32290.16571400.13676922X-RAY DIFFRACTION100
1.3229-1.40580.16161540.13056953X-RAY DIFFRACTION100
1.4058-1.51430.15261480.12217007X-RAY DIFFRACTION100
1.5143-1.66670.1251440.11966963X-RAY DIFFRACTION100
1.6667-1.90790.1321530.11416950X-RAY DIFFRACTION100
1.9079-2.40370.16071600.12886769X-RAY DIFFRACTION97
2.4037-36.81220.14861380.12516804X-RAY DIFFRACTION97

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