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- PDB-8i3z: Crystal structure of NAD-II riboswitch (two strands) with NMN at ... -

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Basic information

Entry
Database: PDB / ID: 8i3z
TitleCrystal structure of NAD-II riboswitch (two strands) with NMN at 1.67 angstrom
Components
  • RNA (31-MER)
  • RNA (5'-R(*AP*GP*AP*GP*CP*GP*UP*UP*GP*CP*GP*UP*CP*CP*GP*AP*AP*AP*GP*UP*(CBV)P*GP*CP*C)-3')
KeywordsRNA / Aptamer
Function / homologyBETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / RNA / RNA (> 10)
Function and homology information
Biological speciesStreptococcus parasanguinis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsPeng, X. / Lilley, D.M.J. / Huang, L.
Funding support China, United Kingdom, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171191 China
Cancer Research UKA18604 United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Crystal structures of the NAD+-II riboswitch reveal two distinct ligand-binding pockets.
Authors: Peng, X. / Liao, W. / Lin, X. / Lilley, D.M.J. / Huang, L.
History
DepositionJan 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*AP*GP*AP*GP*CP*GP*UP*UP*GP*CP*GP*UP*CP*CP*GP*AP*AP*AP*GP*UP*(CBV)P*GP*CP*C)-3')
B: RNA (31-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6018
Polymers17,8392
Non-polymers7626
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-49 kcal/mol
Surface area9550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.271, 81.271, 61.855
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-228-

HOH

21A-233-

HOH

31A-257-

HOH

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Components

#1: RNA chain RNA (5'-R(*AP*GP*AP*GP*CP*GP*UP*UP*GP*CP*GP*UP*CP*CP*GP*AP*AP*AP*GP*UP*(CBV)P*GP*CP*C)-3')


Mass: 7802.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus parasanguinis (bacteria)
#2: RNA chain RNA (31-MER)


Mass: 10036.118 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus parasanguinis (bacteria)
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-NMN / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / NICOTINAMIDE MONONUCLEOTIDE


Mass: 335.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16N2O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 3.52 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.0 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Jan 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.67→46.67 Å / Num. obs: 27501 / % possible obs: 98.99 % / Redundancy: 16 % / Biso Wilson estimate: 25.48 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.014 / Net I/σ(I): 22.6
Reflection shellResolution: 1.67→1.71 Å / Rmerge(I) obs: 0.962 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1875 / CC1/2: 0.892 / Rpim(I) all: 0.387

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Processing

Software
NameVersionClassification
PHENIXdev_4788refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8HB1

8hb1


Resolution: 1.67→30.59 Å / SU ML: 0.1723 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9938
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1856 1369 4.99 %
Rwork0.1679 26091 -
obs0.1688 27460 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.31 Å2
Refinement stepCycle: LAST / Resolution: 1.67→30.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1178 48 146 1372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01241366
X-RAY DIFFRACTIONf_angle_d1.89022124
X-RAY DIFFRACTIONf_chiral_restr0.0853280
X-RAY DIFFRACTIONf_plane_restr0.02159
X-RAY DIFFRACTIONf_dihedral_angle_d17.044662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.730.27531290.23192421X-RAY DIFFRACTION93.07
1.73-1.80.25851260.22552531X-RAY DIFFRACTION97.58
1.8-1.880.23441340.22262629X-RAY DIFFRACTION99.86
1.88-1.980.22461540.20692563X-RAY DIFFRACTION99.89
1.98-2.10.23141100.20742638X-RAY DIFFRACTION100
2.1-2.270.19821390.20182628X-RAY DIFFRACTION99.82
2.27-2.490.21031640.21032587X-RAY DIFFRACTION99.89
2.49-2.850.22621400.212654X-RAY DIFFRACTION99.96
2.86-3.60.22451170.15132681X-RAY DIFFRACTION99.93
3.6-30.590.12581560.12662759X-RAY DIFFRACTION100
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)
10.367398978405-0.127033748724-0.7402453208161.30466650576-0.9101484127911.92299990924-0.117901302633-0.0854538442045-0.252224746103-0.135899145667-0.0220312665768-0.2004195984870.2407975454-0.4953534642250.1192651367390.218757936224-0.01348566290290.004549011534990.3665673187490.07592631214330.4180248684212.415443258230.43672228027.56218770956
26.78640907304-1.37975717845-1.307712091612.87104272611-0.8633964409152.10399810629-0.01654666451580.1759261245370.61540564574-0.01533125681770.0148835631368-0.387225560418-0.08302679591940.2037588456050.002777291713850.189576199996-0.04279580209120.008864187510660.3146662312850.03678671006760.349984466386-5.2484871416634.511395765717.26129716
31.727007908561.62902100673-0.6134609861812.480250517890.1104757083596.64808338258-0.09936115757160.914180546906-0.476900776956-0.5253338968840.0315560335930.02085429426610.4168019031120.06347054518070.03836528706310.3121009890530.0284402484126-0.0416118930530.582756105218-0.1054935204530.308100503058-8.1364586666423.87737217976.53214811091
47.697710147522.48711591721-0.305717047267.9454946844-1.474083895090.544694120308-0.23018362076-0.129618050383-0.492296649291-1.407050900670.0341992062006-0.4133189371160.5855290125361.396551944520.1126794080961.304900219370.208803962166-0.07242043931241.97874842886-0.633779937590.796704169957-4.0741184973614.3227397694-16.2033833459
57.209058839080.09411748585462.570365501810.7291577637980.1843304570363.901803352270.3515759231051.22731020511-0.722288720097-0.141019365030.066594203966-0.4081227398480.4832272430820.0766069068075-0.406582612570.308358049173-0.02384012254220.03243286253280.710358267587-0.01562667392160.4829187405132.447105792430.05181505964.21403677582
64.047312988340.808852480655-0.4889682417870.210940545968-0.06952973295353.36949047313-0.153997518815-0.439109818606-0.1847463245760.07369000713250.200812713349-0.2737876606350.3575766655450.33659199861-0.03189595849240.2488645805550.0421564110974-0.005442370477230.4162962097650.1353814959370.49589224949619.960983815929.096496896312.1381706166
77.16192316577-0.557429294898-0.7948014141792.309626565350.7333076357321.94984188824-0.0324377369201-0.1795476933140.7886607370450.0813600721237-0.0715957807346-0.276798659381-0.01329750969540.1036508317640.1911406319510.207204234748-0.07758507310210.005140557111620.3349860039190.1201845907890.3603703464891.7023335594535.804512592615.8531518757
82.156032599940.9991983410331.327847561965.53085744212-0.1314726953862.697498218960.02688405918560.6876924756780.1010792551060.0517518286451-0.03690026852670.5157978187930.329572326517-0.4504671602860.05614582970460.209539082164-0.0463031274183-0.02675652627220.433832090830.01814982225610.255807392697-19.265663374428.285256914311.6854680351
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 5 )AA1 - 5
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 10 )AA6 - 10
3X-RAY DIFFRACTION3chain 'A' and (resid 11 through 23 )AA11 - 23
4X-RAY DIFFRACTION4chain 'A' and (resid 24 through 24 )AA24
5X-RAY DIFFRACTION5chain 'B' and (resid 27 through 36 )BB27 - 36
6X-RAY DIFFRACTION6chain 'B' and (resid 37 through 41 )BB37 - 41
7X-RAY DIFFRACTION7chain 'B' and (resid 42 through 51 )BB42 - 51
8X-RAY DIFFRACTION8chain 'B' and (resid 52 through 56 )BB52 - 56

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