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

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Basic information

Entry
Database: PDB / ID: 6tff
TitleCrystal structure of the ADP-binding domain of the NAD+ riboswitch with Nicotinamide adenine dinucleotide (NAD+)
ComponentsChains: A
KeywordsRNA / RNA structure / Riboswitch / X-ray crystallography / Non-coding RNA
Function / homologyBROMIDE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / : / RNA / RNA (> 10)
Function and homology information
Biological speciesCandidatus Koribacter versatilis Ellin345 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 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)17,75310
Polymers16,7851
Non-polymers9689
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-47 kcal/mol
Surface area9440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.880, 59.844, 192.026
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

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RNA chain , 1 types, 1 molecules A

#1: RNA chain Chains: A


Mass: 16785.062 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Candidatus Koribacter versatilis Ellin345 (bacteria)
References: GenBank: 94549081

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Non-polymers , 5 types, 18 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 5 Å3/Da / Density % sol: 75 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.2 M Potassium Chloride, 0.1 M Mg Acetate, 0.05 M Sodium Cacodylate pH 6.6, 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: I24 / Wavelength: 0.9186 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9186 Å / Relative weight: 1
ReflectionResolution: 2.52→55.42 Å / Num. obs: 11699 / % possible obs: 99.9 % / Observed criterion σ(I): 0.6 / Redundancy: 6.3 % / Biso Wilson estimate: 73.53 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.034 / Net I/σ(I): 12.6
Reflection shellResolution: 2.52→2.56 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 552 / CC1/2: 0.41 / Rpim(I) all: 1.2 / % 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: 6TF0

6tf0


Resolution: 2.52→55.42 Å / SU ML: 0.4325 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.7641
RfactorNum. reflection% reflection
Rfree0.2251 654 5.65 %
Rwork0.2133 --
obs0.214 11577 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 75.34 Å2
Refinement stepCycle: LAST / Resolution: 2.52→55.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1111 36 9 1156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041273
X-RAY DIFFRACTIONf_angle_d0.89661983
X-RAY DIFFRACTIONf_chiral_restr0.0373263
X-RAY DIFFRACTIONf_plane_restr0.006353
X-RAY DIFFRACTIONf_dihedral_angle_d12.7144633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.710.45041340.43082083X-RAY DIFFRACTION96.77
2.71-2.990.37141300.34582154X-RAY DIFFRACTION99.61
2.99-3.420.23541300.23512156X-RAY DIFFRACTION98.53
3.42-4.30.21111240.19262210X-RAY DIFFRACTION99.53
4.31-55.420.1891360.17972320X-RAY DIFFRACTION99.63

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