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- PDB-7d81: Crystal Structure of the Domain2 of NAD+ Riboswitch with nicotina... -

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Basic information

Entry
Database: PDB / ID: 7d81
TitleCrystal Structure of the Domain2 of NAD+ Riboswitch with nicotinamide adenine dinucleotide (NAD+)
Components832GAAA (50-MER)
KeywordsRNA / riboswitch / RNA structure / RNA folding / RNA-ligand interactions / RNA crystallography
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE / RNA / RNA (> 10)
Function and homology information
Biological speciesAcidobacteriaceae bacterium KBS 83 (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChen, H. / Ren, A.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structural distinctions between NAD+ riboswitch domains 1 and 2 determine differential folding and ligand binding.
Authors: Chen, H. / Egger, M. / Xu, X. / Flemmich, L. / Krasheninina, O. / Sun, A. / Micura, R. / Ren, A.
History
DepositionOct 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Dec 23, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 832GAAA (50-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8405
Polymers16,1041
Non-polymers7364
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-10 kcal/mol
Surface area8780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.026, 76.026, 50.468
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: RNA chain 832GAAA (50-MER)


Mass: 16103.608 Da / Num. of mol.: 1 / Mutation: C2G, A27G, G49C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidobacteriaceae bacterium KBS 83 (unknown)
Production host: in vitro transcription vector pT7-TP(deltai) (unknown)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NaCl 0.1 M CHES pH 9.5, 50% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 10115 / % possible obs: 100 % / Redundancy: 18.9 % / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.019 / Rrim(I) all: 0.083 / Χ2: 0.846 / Net I/σ(I): 5.4 / Num. measured all: 191116
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.1816.21.1329950.8750.2811.1670.438100
2.18-2.2618.50.8589780.9340.2020.8820.522100
2.26-2.3719.40.66610040.9670.1540.6830.458100
2.37-2.4918.20.469920.9870.110.4730.474100
2.49-2.65200.3210060.990.0730.3280.512100
2.65-2.8520.10.21610060.9950.0490.2220.646100
2.85-3.1419.50.11910190.9970.0280.1221.068100
3.14-3.5919.30.09110070.9980.0210.0931.46699.9
3.59-4.5219.60.07110230.9990.0170.0731.661100
4.52-50180.04610850.9990.0110.0481.07799.9

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D7V
Resolution: 2.1→30.364 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 30.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2507 535 5.3 %
Rwork0.2244 9552 -
obs0.2259 10087 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.22 Å2 / Biso mean: 68.8862 Å2 / Biso min: 32.98 Å2
Refinement stepCycle: final / Resolution: 2.1→30.364 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1068 47 27 1142
Biso mean--73.62 52.61 -
Num. residues----50
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.1003-2.31160.3031460.25412327
2.3116-2.64590.36641350.28822350
2.6459-3.33290.32941090.27342410
3.3329-30.3640.20761450.19352465

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