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

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Basic information

Entry
Database: PDB / ID: 8hba
TitleCrystal structure of NAD-II riboswitch (single strand) with NAD
ComponentsRNA (55-MER)
KeywordsRNA / Riboswitch / NAD / NMN / Aptamer
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / RNA / RNA (> 10)
Function and homology information
Biological speciesStreptococcus parasanguinis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 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)
B: RNA (55-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5916
Polymers36,2662
Non-polymers2,3264
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-11 kcal/mol
Surface area15120 Å2
Unit cell
Length a, b, c (Å)37.756, 68.640, 114.009
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain RNA (55-MER)


Mass: 18132.947 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Streptococcus parasanguinis (bacteria)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-NMN / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / NICOTINAMIDE MONONUCLEOTIDE


Mass: 335.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N2O8P / Feature type: SUBJECT OF INVESTIGATION
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: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
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

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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: Sep 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.64→19.61 Å / Num. obs: 9135 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 11.99 % / CC1/2: 0.919 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.016 / Net I/σ(I): 23.3
Reflection shellResolution: 2.64→2.74 Å / Rmerge(I) obs: 0.897 / Mean I/σ(I) obs: 2 / Num. unique obs: 847 / CC1/2: 0.919 / Rpim(I) all: 0.292 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.5refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8HB1

8hb1


Resolution: 2.64→19.61 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.931 / SU B: 43.559 / SU ML: 0.404 / Cross valid method: THROUGHOUT / ESU R Free: 0.397 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27456 934 10.3 %RANDOM
Rwork0.2294 ---
obs0.2339 8168 98.89 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 103.385 Å2
Baniso -1Baniso -2Baniso -3
1-10.64 Å20 Å20 Å2
2---4.23 Å20 Å2
3----6.41 Å2
Refinement stepCycle: LAST / Resolution: 2.64→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2111 154 0 2265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0112600
X-RAY DIFFRACTIONr_bond_other_d0.0030.021039
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.2693935
X-RAY DIFFRACTIONr_angle_other_deg1.6772.9092513
X-RAY DIFFRACTIONr_chiral_restr0.1040.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021361
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02580
X-RAY DIFFRACTIONr_scbond_it2.57.032600
X-RAY DIFFRACTIONr_scbond_other2.57.032601
X-RAY DIFFRACTIONr_scangle_other4.04510.5613936
X-RAY DIFFRACTIONr_long_range_B_refined9.37410101
X-RAY DIFFRACTIONr_long_range_B_other9.37410102
LS refinement shellResolution: 2.642→2.71 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.529 66 -
Rwork0.547 557 -
obs--92.3 %
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)
13.4776-1.96411.334211.9889-2.33797.193-0.2364-0.030.3217-0.7950.0432-0.0058-0.06020.00020.19320.2654-0.0748-0.11460.03630.04020.0924-2.180.244-41.634
22.38721.2511-1.530112.1638-2.60448.0228-0.1360.18710.11120.6163-0.1656-0.3599-0.11410.00920.30170.19290.00120.06240.02770.04210.10161.528-0.305-15.4
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 55
2X-RAY DIFFRACTION2B0 - 55

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