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- PDB-6yml: Crystal structure of the SAM-SAH riboswitch with decarboxylated SAH -

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Basic information

Entry
Database: PDB / ID: 6yml
TitleCrystal structure of the SAM-SAH riboswitch with decarboxylated SAH
Components
  • Chains: A,C
  • Chains: B,D
KeywordsRNA / Pseudoknot / SAM / Riboswitch
Function / homologyADENOSINE MONOPHOSPHATE / 5'-S-(3-aminopropyl)-5'-thioadenosine / RNA / RNA (> 10)
Function and homology information
Biological speciesRoseobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsHuang, L. / Lilley, D.M.J.
Funding support United Kingdom, China, 2items
OrganizationGrant numberCountry
Cancer Research UKA18604 United Kingdom
Ministry of Education (MoE, China) China
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Crystal structure and ligand-induced folding of the SAM/SAH riboswitch.
Authors: Huang, L. / Liao, T.W. / Wang, J. / Ha, T. / Lilley, D.M.J.
History
DepositionApr 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chains: A,C
B: Chains: B,D
C: Chains: A,C
D: Chains: B,D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6958
Polymers22,5714
Non-polymers1,1244
Water905
1
A: Chains: A,C
B: Chains: B,D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0695
Polymers11,2862
Non-polymers7843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Chains: A,C
D: Chains: B,D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6263
Polymers11,2862
Non-polymers3401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.218, 86.218, 75.395
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number149
Space group name H-MP312
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: -y,-x,-z
#5: -x+y,y,-z
#6: x,x-y,-z

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Components

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RNA chain , 2 types, 4 molecules ACBD

#1: RNA chain Chains: A,C


Mass: 8389.874 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Roseobacter sp. (bacteria)
#2: RNA chain Chains: B,D


Mass: 2895.791 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Roseobacter sp. (bacteria)

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Non-polymers , 4 types, 9 molecules

#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#4: Chemical ChemComp-DSH / 5'-S-(3-aminopropyl)-5'-thioadenosine


Mass: 340.401 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H20N6O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.72 Å3/Da / Density % sol: 66.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.01 M Magnesium Sulfate, 0.05 M Sodium Cacodylate pH 6.0, 1.8 M Lithium Sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9188 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9188 Å / Relative weight: 1
ReflectionResolution: 2.17→75.4 Å / Num. obs: 17121 / % possible obs: 100 % / Observed criterion σ(I): 0.6 / Redundancy: 9.7 % / Biso Wilson estimate: 69.42 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.033 / Net I/σ(I): 9.4
Reflection shellResolution: 2.17→2.2 Å / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 867 / CC1/2: 0.355 / Rpim(I) all: 1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YL5

6yl5


Resolution: 2.17→53.05 Å / SU ML: 0.3452 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.1866
RfactorNum. reflection% reflection
Rfree0.2332 725 4.23 %
Rwork0.1983 --
obs0.1998 17121 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 74.95 Å2
Refinement stepCycle: LAST / Resolution: 2.17→53.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1484 70 5 1559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00661731
X-RAY DIFFRACTIONf_angle_d1.48852683
X-RAY DIFFRACTIONf_chiral_restr0.1262356
X-RAY DIFFRACTIONf_plane_restr0.010673
X-RAY DIFFRACTIONf_dihedral_angle_d17.548857
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.330.35361260.2993156X-RAY DIFFRACTION96.13
2.33-2.570.39891720.31923230X-RAY DIFFRACTION100
2.57-2.940.36781410.33473318X-RAY DIFFRACTION100
2.94-3.70.28641300.22433317X-RAY DIFFRACTION100
3.7-53.050.1731560.14753375X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: 20.5268773692 Å / Origin y: -28.5433780996 Å / Origin z: 17.9665400538 Å
111213212223313233
T0.792646920848 Å2-0.0282211245561 Å2-0.00305360737992 Å2-0.611988832929 Å20.0299842351869 Å2--0.75943010969 Å2
L-0.602024258174 °20.181644062808 °20.15970629244 °2-0.264042713503 °20.0681717530977 °2---0.233417418023 °2
S0.0258798603246 Å °-0.031269661099 Å °0.00601602852387 Å °-0.111139223502 Å °-0.160528492185 Å °0.082266351334 Å °-0.0299861146124 Å °0.0429710393775 Å °-0.0022242663072 Å °
Refinement TLS groupSelection details: all

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