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- PDB-6tfh: Crystal structure of the ADP-binding domain of the NAD+ riboswitc... -

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Basic information

Entry
Database: PDB / ID: 6tfh
TitleCrystal structure of the ADP-binding domain of the NAD+ riboswitch with Nicotinamide adenine dinucleotide, reduced (NADH); soaking with Manganese(II) (Mn2+)
ComponentsChains: A
KeywordsRNA / RNA structure / Riboswitch / X-ray crystallography / Non-coding RNA
Function / homology: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / RNA / RNA (> 10)
Function and homology information
Biological speciesCandidatus Koribacter versatilis Ellin345 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsHuang, L. / Lilley, D.M.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKA18604 United Kingdom
CitationJournal: Rna / Year: 2020
Title: Structure and ligand binding of the ADP-binding domain of the NAD+ riboswitch.
Authors: Huang, L. / Wang, J. / Lilley, D.M.J.
History
DepositionNov 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 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

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Assembly

Deposited unit
A: Chains: A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,04512
Polymers16,8641
Non-polymers1,18111
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-55 kcal/mol
Surface area9250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.935, 58.360, 193.968
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: RNA chain Chains: A


Mass: 16863.957 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Candidatus Koribacter versatilis Ellin345 (bacteria)
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
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: 5 Å3/Da / Density % sol: 75 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.2 M Potassium Chloride, 0.1 M Mg Acetate, 0.05 M Sodium Cacodylate pH 6.8, 10% w/v Polyethylene Glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.8923 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8923 Å / Relative weight: 1
ReflectionResolution: 2.95→48.5 Å / Num. obs: 12163 / % possible obs: 96.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 93.67 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.059 / Net I/σ(I): 10.8
Reflection shellResolution: 2.95→3 Å / Rmerge(I) obs: 2.7 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 359 / CC1/2: 0.48 / Rpim(I) all: 1.8

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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: 6TF0

6tf0


Resolution: 2.95→48.49 Å / SU ML: 0.5932 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.5261
RfactorNum. reflection% reflection
Rfree0.2663 616 5.06 %
Rwork0.2213 --
obs0.2234 12163 92.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 113.5 Å2
Refinement stepCycle: LAST / Resolution: 2.95→48.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1112 39 0 1151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01151275
X-RAY DIFFRACTIONf_angle_d1.94971986
X-RAY DIFFRACTIONf_chiral_restr0.0754262
X-RAY DIFFRACTIONf_plane_restr0.010953
X-RAY DIFFRACTIONf_dihedral_angle_d15.8029624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.250.46761650.43782862X-RAY DIFFRACTION91.87
3.25-3.720.4361660.3342831X-RAY DIFFRACTION91.4
3.72-4.690.22621580.22412900X-RAY DIFFRACTION93.8
4.69-48.490.19561270.15832954X-RAY DIFFRACTION93.39

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