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- PDB-6tf2: Crystal structure of the ADP-binding domain of the NAD+ riboswitc... -

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Basic information

Entry
Database: PDB / ID: 6tf2
TitleCrystal structure of the ADP-binding domain of the NAD+ riboswitch with Adenosine 5-triphosphate (ATP)
ComponentsChains: A
KeywordsRNA / RNA structure / Riboswitch / X-ray crystallography
Function / homologyADENOSINE-5'-TRIPHOSPHATE / BROMIDE ION / : / RNA / RNA (> 10)
Function and homology information
Biological speciesCandidatus Koribacter versatilis Ellin345 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 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 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)17,59710
Polymers16,7851
Non-polymers8129
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-47 kcal/mol
Surface area9320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.410, 59.030, 190.980
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, 13 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


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 5.02 Å3/Da / Density % sol: 75.5 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop
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: 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: 2.49→54.98 Å / Num. obs: 20079 / % possible obs: 98.7 % / Redundancy: 6.27 % / Biso Wilson estimate: 77.49 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.024 / Net I/σ(I): 18.21
Reflection shellResolution: 2.49→2.53 Å / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 563 / CC1/2: 0.35 / Rpim(I) all: 1 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
xia2data reduction
xia2data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.55→54.98 Å / SU ML: 0.4709 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.2513
RfactorNum. reflection% reflection
Rfree0.2385 898 4.47 %
Rwork0.2071 --
obs0.2085 20079 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 84.59 Å2
Refinement stepCycle: LAST / Resolution: 2.55→54.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1111 39 4 1154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00661276
X-RAY DIFFRACTIONf_angle_d1.38331989
X-RAY DIFFRACTIONf_chiral_restr0.0587263
X-RAY DIFFRACTIONf_plane_restr0.008253
X-RAY DIFFRACTIONf_dihedral_angle_d14.5623633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.710.4781670.4723176X-RAY DIFFRACTION98.7
2.71-2.920.40241380.36463235X-RAY DIFFRACTION98.74
2.92-3.210.31221700.28853109X-RAY DIFFRACTION96.19
3.21-3.680.26431750.21023130X-RAY DIFFRACTION97.01
3.68-4.630.17971150.16883266X-RAY DIFFRACTION99.18
4.63-54.980.19291330.1713265X-RAY DIFFRACTION99.1

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