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

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Basic information

Entry
Database: PDB / ID: 6tfe
TitleCrystal structure of the ADP-binding domain of the NAD+ riboswitch with N6-Methyl-adenosine-5'-triphosphate (m6ATP)
ComponentsChains: A
KeywordsRNA / RNA structure / Riboswitch / X-ray crystallography / Non-coding RNA
Function / homologyBROMIDE ION / N6-Methyladenosine 5'-triphosphate / : / RNA / RNA (> 10)
Function and homology information
Biological speciesCandidatus Koribacter versatilis Ellin345 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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 1.1May 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)17,80118
Polymers16,7851
Non-polymers1,01617
Water45025
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-95 kcal/mol
Surface area9510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.350, 59.440, 190.070
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, 42 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-N6E / N6-Methyladenosine 5'-triphosphate


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 7.2
Details: 0.2 M Potassium Chloride, 0.1 M Mg Acetate, 0.05 M Sodium Cacodylate pH 7.2, 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: 2.3→47.52 Å / Num. obs: 27515 / % possible obs: 99.17 % / Redundancy: 6.3 % / Biso Wilson estimate: 71.97 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.023 / Net I/σ(I): 16.1
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 1.82 / Mean I/σ(I) obs: 1 / Num. unique obs: 697 / CC1/2: 0.59 / Rpim(I) all: 0.76

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→47.52 Å / SU ML: 0.4149 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.6475
RfactorNum. reflection% reflection
Rfree0.2571 1391 5.06 %
Rwork0.2394 --
obs0.2403 27515 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 98.85 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1111 48 25 1184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651277
X-RAY DIFFRACTIONf_angle_d1.09871990
X-RAY DIFFRACTIONf_chiral_restr0.0488263
X-RAY DIFFRACTIONf_plane_restr0.008153
X-RAY DIFFRACTIONf_dihedral_angle_d11.8046636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.380.46881620.44442570X-RAY DIFFRACTION98.88
2.38-2.480.49531260.40772635X-RAY DIFFRACTION98.93
2.48-2.590.461210.39062659X-RAY DIFFRACTION99.5
2.59-2.730.42781240.38232662X-RAY DIFFRACTION99.61
2.73-2.90.38461280.35192583X-RAY DIFFRACTION98.83
2.9-3.120.29921730.27412575X-RAY DIFFRACTION97.38
3.12-3.440.22291040.24762621X-RAY DIFFRACTION97.6
3.44-3.930.28541450.22652593X-RAY DIFFRACTION98.63
3.93-4.950.25881480.2132619X-RAY DIFFRACTION98.93
4.95-47.520.18541600.18912607X-RAY DIFFRACTION98.75

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