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- PDB-6tf1: Crystal structure of the ADP-binding domain of the NAD+ riboswitc... -

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Basic information

Entry
Database: PDB / ID: 6tf1
TitleCrystal structure of the ADP-binding domain of the NAD+ riboswitch with Adenosine diphosphate (ADP)
ComponentsChains: A
KeywordsRNA / RNA structure / tRNA-mimicking / X-ray crystallography
Function / homologyADENOSINE-5'-DIPHOSPHATE / : / RNA / RNA (> 10)
Function and homology information
Biological speciesCandidatus Koribacter versatilis Ellin345 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.1Jan 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)17,40510
Polymers16,7851
Non-polymers6209
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-62 kcal/mol
Surface area9240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.585, 59.014, 190.587
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: 16785.062 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Candidatus Koribacter versatilis Ellin345 (bacteria)
References: GenBank: 94549081
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / 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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
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 / pH: 7
Details: 0.2 M Potassium Chloride, 0.1 M Mg Acetate, 0.05 M Sodium Cacodylate pH 7.0, 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: 2.23→56.37 Å / Num. obs: 16012 / % possible obs: 98.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 69.65 Å2 / CC1/2: 0.97 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.042 / Net I/σ(I): 9.5
Reflection shellResolution: 2.23→2.27 Å / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.2 / Num. unique obs: 787 / CC1/2: 0.78 / Rpim(I) all: 1 / % possible all: 96.4

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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: 2.4→56.37 Å / SU ML: 0.3598 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.78
RfactorNum. reflection% reflection
Rfree0.2447 622 4.95 %
Rwork0.2157 --
obs0.2172 12553 95.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 77.57 Å2
Refinement stepCycle: LAST / Resolution: 2.4→56.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1111 35 18 1164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081272
X-RAY DIFFRACTIONf_angle_d1.60931982
X-RAY DIFFRACTIONf_chiral_restr0.0633263
X-RAY DIFFRACTIONf_plane_restr0.009353
X-RAY DIFFRACTIONf_dihedral_angle_d13.8411631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.640.44061570.46472675X-RAY DIFFRACTION88.2
2.64-3.020.41881620.36482985X-RAY DIFFRACTION97.19
3.02-3.810.27391430.2253039X-RAY DIFFRACTION97.16
3.81-56.370.18571600.16893232X-RAY DIFFRACTION99.21

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