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- PDB-6tf0: Crystal structure of the ADP-binding domain of the NAD+ riboswitc... -

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Basic information

Entry
Database: PDB / ID: 6tf0
TitleCrystal structure of the ADP-binding domain of the NAD+ riboswitch with Nicotinamide adenine dinucleotide, reduced (NADH)
ComponentsChains: A
KeywordsRNA / RNA structure / tRNA-mimicking / X-ray crystallography
Function / homology1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / RNA / RNA (> 10)
Function and homology information
Biological speciesCandidatus Koribacter versatilis Ellin345 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 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

Downloads & links

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Assembly

Deposited unit
A: Chains: A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,77012
Polymers16,8641
Non-polymers90611
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-72 kcal/mol
Surface area9370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.272, 59.230, 191.085
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: 16863.957 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Candidatus Koribacter versatilis Ellin345 (bacteria)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 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 (30% PEG200)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9195 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9195 Å / Relative weight: 1
ReflectionResolution: 2.1→32.11 Å / Num. obs: 36174 / % possible obs: 98.81 % / Observed criterion σ(I): 1.2 / Redundancy: 6.6 % / Biso Wilson estimate: 65.88 Å2 / CC1/2: 0.8 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.016 / Net I/σ(I): 18.1
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 1.44 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 939 / CC1/2: 0.8 / Rpim(I) all: 0.59

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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: 2.1→32.11 Å / SU ML: 0.3171 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.5277
RfactorNum. reflection% reflection
Rfree0.2577 1650 4.56 %
Rwork0.21 --
obs0.2118 36174 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 83.13 Å2
Refinement stepCycle: LAST / Resolution: 2.1→32.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1112 39 25 1176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00921275
X-RAY DIFFRACTIONf_angle_d1.65191986
X-RAY DIFFRACTIONf_chiral_restr0.0718262
X-RAY DIFFRACTIONf_plane_restr0.013853
X-RAY DIFFRACTIONf_dihedral_angle_d14.6775624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.50521320.46522867X-RAY DIFFRACTION98.07
2.16-2.230.4231630.46592860X-RAY DIFFRACTION97.9
2.23-2.310.41491580.37642835X-RAY DIFFRACTION98.42
2.31-2.40.371560.34362820X-RAY DIFFRACTION98.15
2.4-2.510.32331530.31112869X-RAY DIFFRACTION98.6
2.51-2.650.39671200.32262899X-RAY DIFFRACTION98.66
2.65-2.810.29961390.30752895X-RAY DIFFRACTION98.86
2.81-3.030.36831640.28142839X-RAY DIFFRACTION98.72
3.03-3.330.29151330.22732859X-RAY DIFFRACTION97.78
3.33-3.810.22461300.20142894X-RAY DIFFRACTION99.08
3.81-4.80.1771060.16252936X-RAY DIFFRACTION99.48
4.8-32.110.2192960.15842951X-RAY DIFFRACTION99.22
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.87500299987-0.4063689257661.798986230273.13664615623-0.4339850295644.583828479910.2583878410740.796265024191-0.296046954452-0.3110672917430.01720494193910.3767400548610.0830778096058-0.297575017796-0.2567476648170.4702119701860.05053289417620.04057505304130.68894104816-0.01956788511290.53530035380816.0606243714-1.6814054401522.2190289195
2-0.0411265014649-2.21774542794-1.332649328887.699982897126.997898187675.508456480420.0102636735289-0.3486203402470.648626508357-0.1959900128560.098119979263-0.310287222748-0.567742110878-0.138011578304-0.028369202240.8065051948940.02932876541270.06389408908270.864014735294-0.1071236635520.7645561812279.8815265259410.521643731645.9524959742
33.68507111652-0.06214517740491.415795524132.68145242149-1.092210154292.974478492010.09578980253740.5583119108740.0530617563692-0.2257024377280.1317583867030.305263080849-0.0463395464095-0.630822301843-0.2198393742530.5053952365550.088394329587-0.009467652540540.893925457637-0.00969890050840.62262047236311.1682034749-1.7017513032819.5584857813
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 36 )
3X-RAY DIFFRACTION3chain 'A' and (resid 37 through 52 )

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