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- PDB-6tf3: Crystal structure of the ADP-binding domain of the NAD+ riboswitc... -

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Basic information

Entry
Database: PDB / ID: 6tf3
TitleCrystal structure of the ADP-binding domain of the NAD+ riboswitch with Cordycepin 5-triphosphate (3-dATP)
ComponentsChains: A
KeywordsRNA / RNA structure / Riboswitch / X-ray crystallography
Function / homology3'-DEOXYADENOSINE-5'-TRIPHOSPHATE / : / RNA / RNA (> 10)
Function and homology information
Biological speciesCandidatus Koribacter versatilis Ellin345 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 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 13, 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)17,46510
Polymers16,7851
Non-polymers6809
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-69 kcal/mol
Surface area9320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.530, 58.150, 191.140
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.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-3AT / 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE / CORDYCEPIN TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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 Å3/Da / Density % sol: 75 %
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 6.2, 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: 2.66→55.09 Å / Num. obs: 9451 / % possible obs: 98.3 % / Redundancy: 6.32 % / Biso Wilson estimate: 77.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.031 / Net I/σ(I): 14.9
Reflection shellResolution: 2.66→2.71 Å / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1 / Num. unique obs: 463 / CC1/2: 0.49 / Rpim(I) all: 0.86

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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: 2.66→55.09 Å / SU ML: 0.479 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.3602
RfactorNum. reflection% reflection
Rfree0.2414 492 5.22 %
Rwork0.2116 --
obs0.2134 9432 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 87.58 Å2
Refinement stepCycle: LAST / Resolution: 2.66→55.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1111 34 2 1147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631271
X-RAY DIFFRACTIONf_angle_d1.04971980
X-RAY DIFFRACTIONf_chiral_restr0.045262
X-RAY DIFFRACTIONf_plane_restr0.007153
X-RAY DIFFRACTIONf_dihedral_angle_d12.0611622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.930.50631410.43372187X-RAY DIFFRACTION98.77
2.93-3.350.26521030.27612157X-RAY DIFFRACTION96.01
3.35-4.220.22831250.19172220X-RAY DIFFRACTION98.28
4.22-55.090.20491230.182376X-RAY DIFFRACTION99.28

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