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- PDB-8hb8: Crystal structure of NAD-II riboswitch (single strand) with NMN -

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Basic information

Entry
Database: PDB / ID: 8hb8
TitleCrystal structure of NAD-II riboswitch (single strand) with NMN
ComponentsRNA (55-MER)
KeywordsRNA / Riboswitch / NAD / NMN / Aptamer
Function / homology: / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / RNA / RNA (> 10)
Function and homology information
Biological speciesStreptococcus parasanguinis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (55-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,46010
Polymers17,8281
Non-polymers1,6329
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-50 kcal/mol
Surface area9510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.362, 121.362, 109.055
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: RNA chain RNA (55-MER)


Mass: 17827.766 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus parasanguinis (bacteria)
#2: 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
#3: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ba
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: 5.6 Å3/Da / Density % sol: 78.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.012 M Sodium chloride, 0.08 M Potassium chloride 0.04 M Sodium cacodylate trihydrate pH 5.5 45% v/v (+/-)-2-Methyl-2,4-pentanediol 0.02 M Hexammine cobalt(III) chloride Soaking with BaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 17176 / % possible obs: 93.2 % / Observed criterion σ(I): 1 / Redundancy: 13.3 % / Biso Wilson estimate: 70.63 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.017 / Net I/σ(I): 26.6
Reflection shellResolution: 2.3→2.42 Å / Rmerge(I) obs: 3.4 / Mean I/σ(I) obs: 1 / Num. unique obs: 2642 / CC1/2: 0.642 / Rpim(I) all: 0.75

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8HB1

8hb1


Resolution: 2.3→27.26 Å / SU ML: 0.6039 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.4222
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2531 853 4.99 %
Rwork0.2271 16227 -
obs0.2284 17080 92.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.23 Å2
Refinement stepCycle: LAST / Resolution: 2.3→27.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1167 51 0 1218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021354
X-RAY DIFFRACTIONf_angle_d0.63822106
X-RAY DIFFRACTIONf_chiral_restr0.0302281
X-RAY DIFFRACTIONf_plane_restr0.003957
X-RAY DIFFRACTIONf_dihedral_angle_d16.4374671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.440.50041570.43472823X-RAY DIFFRACTION99.33
2.44-2.630.43421440.40732869X-RAY DIFFRACTION99.54
2.63-2.90.37931120.34492166X-RAY DIFFRACTION75.26
2.9-3.320.27421460.24872874X-RAY DIFFRACTION99.37
3.32-4.170.22751260.20312451X-RAY DIFFRACTION83.59
4.18-27.260.21781680.19093044X-RAY DIFFRACTION99.94
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)
14.62147586155-0.280014841811-1.053675387980.7500364136221.329991521532.65488694384-0.3025655527991.45071368064-0.651929845958-1.11277753982-0.2980670117560.808252618341-1.361723066240.2638406494110.5795004458321.21323408592-0.2956170140580.1261366543751.08305260944-0.1702702870230.958214055849-3.11699303823-8.56380098346-18.1608984746
22.348336412530.302418940366-0.5029293928411.867517851340.1597818165013.055925657580.1146576317710.28583996164-0.235092756234-0.3333393037350.158351711417-0.194400336757-0.3485395401060.687368506096-0.3121974152820.713255837482-0.0798112677843-0.03335088837140.881848035934-0.05225533641970.743852957497-16.6387615126-24.4080847127-15.9744699885
31.598974016210.1943900970941.621064713382.547282042491.115391474852.703753644260.1876704805610.397651259930.0975528153892-0.5128456382910.13586070116-0.687745489002-0.3321943218450.924467177446-0.1534538423051.0844810222-0.2584510594450.1832214075491.22058419022-0.0832918105390.875848519719-6.53481949508-14.7360725553-21.7205895879
43.55627754207-0.501548398215-0.5137352221032.087512324080.9796535946073.006020291530.1297022223880.3183260840820.0149691361608-0.15112734612-0.3220728216780.1835419956160.0692523097302-0.5115919966290.08443118414890.781822109026-0.0460108860547-0.01387257408350.7130712897730.006440773961360.64548379934-22.6651530116-20.5314264046-14.781621282
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 21 )AA6 - 21
3X-RAY DIFFRACTION3chain 'A' and (resid 22 through 45 )AA22 - 45
4X-RAY DIFFRACTION4chain 'A' and (resid 46 through 55 )AA46 - 55

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