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- PDB-8hb1: Crystal structure of NAD-II riboswitch (two strands) with NMN -

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Basic information

Entry
Database: PDB / ID: 8hb1
TitleCrystal structure of NAD-II riboswitch (two strands) with NMN
Components
  • RNA (30-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 / SAD / Resolution: 2.23 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
DepositionOct 27, 2022Deposition 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 (30-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2778
Polymers17,5092
Non-polymers7686
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-46 kcal/mol
Surface area9240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.314, 82.314, 63.248
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

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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 (30-MER)


Mass: 9706.913 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus parasanguinis (bacteria)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#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.: 1 / 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: 3.69 Å3/Da / Density % sol: 66.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / 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: 0.91908 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Aug 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91908 Å / Relative weight: 1
ReflectionResolution: 2.23→47.31 Å / Num. obs: 12413 / % possible obs: 100 % / Redundancy: 19.2 % / Biso Wilson estimate: 43.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.017 / Net I/σ(I): 22.4
Reflection shellResolution: 2.23→2.29 Å / Rmerge(I) obs: 0.849 / Num. unique obs: 900 / CC1/2: 0.973 / Rpim(I) all: 0.224 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.23→35.64 Å / SU ML: 0.4406 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.0463
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2496 592 4.95 %
Rwork0.2263 11361 -
obs0.2274 11953 96.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.24 Å2
Refinement stepCycle: LAST / Resolution: 2.23→35.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1157 48 1 1206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00931342
X-RAY DIFFRACTIONf_angle_d1.93152088
X-RAY DIFFRACTIONf_chiral_restr0.0781275
X-RAY DIFFRACTIONf_plane_restr0.010458
X-RAY DIFFRACTIONf_dihedral_angle_d15.4337651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.450.55691470.54652489X-RAY DIFFRACTION86.77
2.45-2.810.39611560.37912891X-RAY DIFFRACTION99.38
2.81-3.540.27811460.2432936X-RAY DIFFRACTION99.77
3.54-35.640.1741430.1593045X-RAY DIFFRACTION99.66
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)
11.619896351590.0797403919546-1.62979388125.3918681692-4.317762653451.69933082538-0.177361798040.2050982795210.3047191136520.2524292451420.189149121295-0.158851322597-0.243297310453-0.006454070063530.02501656716240.614560400658-0.113995016434-0.09578873062890.3548728964390.0231195240270.572001348052-28.158517601814.75359616614.33186085388
24.38371559165-0.9910344416822.815992615458.668769978214.253640192914.65959488331-0.5105470514431.75823879234-1.25283979809-1.694421625980.216453609857-0.9653210197850.3999586149790.830237350178-0.07363127601681.10768613393-0.362806707860.275843395440.898542737151-0.3569361308070.943544574708-23.14585555064.79593425885-5.28499589579
35.03575759111.02552541747-3.760570007276.58093771658-0.4741799399774.15801269247-0.5241738360631.599308279310.130670158419-1.519999207420.850526775114-1.82874694396-0.2151920257220.458958134758-0.2606319122411.59821399816-0.148653460490.3887317695611.26554642273-0.1932132381250.899357343601-20.45704788844.81076069803-24.0794174245
46.81857663239-1.30892616058-1.040125897433.60533386767-0.7269044134854.479404168571.35765118981.10261734077-0.3883141877752.09253613295-0.833043832437-0.3401722089791.077674532730.627246744609-0.2127240026321.42907354311-0.1559601826290.2818303131861.24865544561-0.4078434051621.1372297373-17.64497582818.38900022563-16.2630505171
52.948608101241.26187994908-1.935950444435.93930791942-0.430681259692.959075248570.329134351673-0.1504415668290.7731324122630.62672316937-0.0116577602118-0.617303122756-0.4742301573310.421690023983-0.2904133209050.800858834431-0.16639483202-0.1816786370510.4458015904310.07103250230810.993947947601-23.555685110826.2730053444.12547911831
64.508222975191.79956870634-2.811248416238.478753384554.070876918785.14111778188-0.1859932138080.706595895461.09149096473-0.4891192395950.2800843104560.568636287302-1.06474425513-0.6160124648830.1886446526980.701043955404-0.00783327476687-0.1322684145310.4632526440890.1305328947480.674840510334-37.982701765216.80919975232.90309907698
73.577201335490.3509117172920.5788886898749.73678432076-0.9993078022660.265888266025-0.04532440132640.134124117953-0.57963529461-0.8331580877110.05046114769590.1695808880231.47780036262-0.6251924304940.08516085557650.876002034193-0.271556556621-0.02659543836330.417966256896-0.03195485503340.453677747852-33.69229726981.80347858761-0.401409982734
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 15 )AA1 - 15
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 20 )AA16 - 20
3X-RAY DIFFRACTION3chain 'A' and (resid 22 through 24 )AA22 - 24
4X-RAY DIFFRACTION4chain 'B' and (resid 26 through 30 )BB26 - 30
5X-RAY DIFFRACTION5chain 'B' and (resid 31 through 45 )BB31 - 45
6X-RAY DIFFRACTION6chain 'B' and (resid 46 through 50 )BB46 - 50
7X-RAY DIFFRACTION7chain 'B' and (resid 51 through 55 )BB51 - 55

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