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- PDB-5kpy: Structure of a 5-hydroxytryptophan aptamer -

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Basic information

Entry
Database: PDB / ID: 5kpy
TitleStructure of a 5-hydroxytryptophan aptamer
Components5-hydroxytryptophan RNA aptamer
KeywordsRNA / aptamer / riboswitch / 5-hydroxytryptophan
Function / homology5-hydroxy-L-tryptophan / IRIDIUM HEXAMMINE ION / RNA / RNA (> 10)
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2 Å
AuthorsBatey, R.T. / Porter, E. / Merck, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1150834 United States
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Recurrent RNA motifs as scaffolds for genetically encodable small-molecule biosensors.
Authors: Porter, E.B. / Polaski, J.T. / Morck, M.M. / Batey, R.T.
History
DepositionJul 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Mar 1, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5-hydroxytryptophan RNA aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,73220
Polymers22,8341
Non-polymers3,89919
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.553, 26.594, 63.367
Angle α, β, γ (deg.)90.00, 106.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain 5-hydroxytryptophan RNA aptamer


Mass: 22833.549 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#2: Chemical ChemComp-4PQ / 5-hydroxy-L-tryptophan / Oxitriptan


Type: L-peptide linking / Mass: 220.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O3 / Comment: neurotransmitter*YM
#3: Chemical
ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: H18IrN6
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 8-14% MPD, 40 mM sodium cacodylate, pH 5.5, 4 mM MgCl2, 12 mM NaCl, 80 mM KCl, 4-9 mM cobalt hexamine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→19.95 Å / Num. obs: 13725 / % possible obs: 96.2 % / Redundancy: 4.34 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 11.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.65 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 5.4 / % possible all: 73.8

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
CrystalCleardata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2→18.333 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 24.97
RfactorNum. reflection% reflection
Rfree0.2581 1372 10 %
Rwork0.2165 --
obs0.2206 13725 96.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→18.333 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1513 106 112 1731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071780
X-RAY DIFFRACTIONf_angle_d1.3082837
X-RAY DIFFRACTIONf_dihedral_angle_d15.167851
X-RAY DIFFRACTIONf_chiral_restr0.047356
X-RAY DIFFRACTIONf_plane_restr0.00773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.07140.26031040.2013940X-RAY DIFFRACTION75
2.0714-2.15420.22561380.21081236X-RAY DIFFRACTION98
2.1542-2.25210.23091340.21681209X-RAY DIFFRACTION96
2.2521-2.37060.3291410.21471268X-RAY DIFFRACTION99
2.3706-2.51880.28611370.2221228X-RAY DIFFRACTION98
2.5188-2.71270.2711400.23381259X-RAY DIFFRACTION99
2.7127-2.98460.31951430.23081291X-RAY DIFFRACTION99
2.9846-3.41410.26381410.21211270X-RAY DIFFRACTION100
3.4141-4.29230.21491450.19011300X-RAY DIFFRACTION100
4.2923-18.3340.25211490.23051352X-RAY DIFFRACTION100

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