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- PDB-5uza: Adenine riboswitch aptamer domain labelled with iodo-uridine by p... -

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Basic information

Entry
Database: PDB / ID: 5uza
TitleAdenine riboswitch aptamer domain labelled with iodo-uridine by position-selective labelling of RNA (PLOR)
ComponentsRNA (71-MER)
KeywordsRNA / adenine riboswitch / iodo-uridine
Function / homologyADENINE / RNA / RNA (> 10)
Function and homology information
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.22 Å
AuthorsLiu, Y. / Stagno, J.R. / Wang, Y.-X.
CitationJournal: Nat Protoc / Year: 2018
Title: Incorporation of isotopic, fluorescent, and heavy-atom-modified nucleotides into RNAs by position-selective labeling of RNA.
Authors: Liu, Y. / Holmstrom, E. / Yu, P. / Tan, K. / Zuo, X. / Nesbitt, D.J. / Sousa, R. / Stagno, J.R. / Wang, Y.X.
History
DepositionFeb 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Mar 6, 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
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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_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.value / _struct_conn.conn_type_id / _struct_conn.id / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: RNA (71-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1475
Polymers22,9391
Non-polymers2084
Water99155
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.985, 151.575, 24.735
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: RNA chain RNA (71-MER)


Mass: 22939.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio vulnificus (bacteria)
#2: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 50mM Tris-HCl (pH:8.5), 100mM KCl, 10mM MgCl2 and 30% Polyethylene Glycol 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.55 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.55 Å / Relative weight: 1
ReflectionResolution: 2.22→46.611 Å / Num. obs: 17080 / % possible obs: 99.7 % / Redundancy: 8.5 % / Biso Wilson estimate: 36.44 Å2 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.017 / Rrim(I) all: 0.051 / Χ2: 0.96 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.22-2.35.20.6580.7750.3070.7290.7799.3
2.3-2.397.60.5840.8960.2250.6270.79299.9
2.39-2.590.4210.9550.1480.4470.849100
2.5-2.639.20.290.9780.1010.3070.894100
2.63-2.89.30.1750.9850.0610.1850.901100
2.8-3.019.20.090.9960.0310.0950.92100
3.01-3.329.20.040.9980.0140.0421.062100
3.32-3.89.10.0310.9980.0110.0331.055100
3.8-4.7890.0270.9980.0090.0291.091100
4.78-5080.0290.9980.0110.0311.13898.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIXdev_2447refinement
PDB_EXTRACT3.22data extraction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.22→46.611 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.17 / Phase error: 25.45
RfactorNum. reflection% reflection
Rfree0.2509 851 4.98 %
Rwork0.2152 --
obs0.217 17080 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.74 Å2 / Biso mean: 42.0833 Å2 / Biso min: 14.21 Å2
Refinement stepCycle: final / Resolution: 2.22→46.611 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1505 17 55 1577
Biso mean--26.09 35.38 -
Num. residues----71
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051705
X-RAY DIFFRACTIONf_angle_d0.3862630
X-RAY DIFFRACTIONf_chiral_restr0.023353
X-RAY DIFFRACTIONf_plane_restr0.00272
X-RAY DIFFRACTIONf_dihedral_angle_d11.521833
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2196-2.35860.34561070.29122307241484
2.3586-2.54070.34571520.297127902942100
2.5407-2.79640.32441590.298627922951100
2.7964-3.2010.29941500.243627732923100
3.201-4.03250.2281400.185728042944100
4.0325-46.62160.17551430.16022763290699
Refinement TLS params.Method: refined / Origin x: -21.431 Å / Origin y: 19.2257 Å / Origin z: -11.1448 Å
111213212223313233
T0.2233 Å2-0.0025 Å2-0.0438 Å2-0.1851 Å20.0366 Å2--0.1505 Å2
L1.6717 °20.0599 °2-0.3413 °2-2.2219 °20.0333 °2--0.4157 °2
S0.0205 Å °0.0537 Å °-0.298 Å °0.0224 Å °-0.0226 Å °-0.3009 Å °-0.0433 Å °-0.0878 Å °0.0232 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allX13 - 83
2X-RAY DIFFRACTION1allX101
3X-RAY DIFFRACTION1allX102 - 104
4X-RAY DIFFRACTION1allC1 - 97

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