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- PDB-7d82: Crystal Structure of the Domain2 of NAD+ Riboswitch with nicotina... -

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Basic information

Entry
Database: PDB / ID: 7d82
TitleCrystal Structure of the Domain2 of NAD+ Riboswitch with nicotinamide adenine dinucleotide (NAD+), soaked in Mn2+
Components832GAAA (50-MER)
KeywordsRNA / riboswitch / RNA structure / RNA folding / RNA-ligand interactions / RNA crystallography
Function / homology: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / RNA / RNA (> 10)
Function and homology information
Biological speciesAcidobacteriaceae bacterium KBS 83 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.489 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
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)17,32216
Polymers16,1041
Non-polymers1,21815
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-6 kcal/mol
Surface area8650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.916, 75.916, 50.289
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 (bacteria)
Production host: in vitro transcription vector pT7-TP(deltai) (others)
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mn / 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: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.6 Å3/Da / Density % sol: 52.65 %
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: 1.2398 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2398 Å / Relative weight: 1
ReflectionResolution: 2.489→30 Å / Num. obs: 11307 / % possible obs: 99.5 % / Redundancy: 19.2 % / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.047 / Rrim(I) all: 0.21 / Χ2: 0.547 / Net I/σ(I): 2.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.5416.21.8693040.7730.4741.930.43796.8
2.54-2.5919.82.0652820.6940.4732.120.397100
2.59-2.6420.41.4353080.8520.3241.4710.412100
2.64-2.6920.11.3783060.9020.3131.4140.411100
2.69-2.7520.21.3722850.8550.3121.4080.413100
2.75-2.8220.11.1453070.9030.2611.1750.411100
2.82-2.89200.8712920.9440.1990.8940.448100
2.89-2.9619.90.6333050.9570.1450.650.449100
2.96-3.0519.80.4973040.9670.1140.510.496100
3.05-3.1519.60.3863050.9770.0880.3970.536100
3.15-3.2619.20.3442920.9820.080.3530.569100
3.26-3.3918.30.2873100.9850.0680.2950.567100
3.39-3.5516.10.2662860.9790.0680.2750.61697.9
3.55-3.7318.50.2032960.9930.0480.2090.65396.7
3.73-3.9720.30.1733160.9950.0390.1770.687100
3.97-4.2720.20.1442940.9950.0330.1470.652100
4.27-4.7200.1233180.9970.0280.1260.699100
4.7-5.3819.10.0943110.9990.0220.0960.658100
5.38-6.7617.10.0823100.9980.020.0850.56298.4
6.76-3018.60.0823440.9980.0190.0840.83999.7

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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

7d7v


Resolution: 2.489→27.516 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2713 550 4.86 %
Rwork0.2213 10757 -
obs0.2238 11307 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.68 Å2 / Biso mean: 59.5885 Å2 / Biso min: 30.8 Å2
Refinement stepCycle: final / Resolution: 2.489→27.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1068 58 36 1162
Biso mean--59.97 50.43 -
Num. residues----50
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.489-2.7390.33971400.2997267098
2.739-3.13490.3221390.24042721100
3.1349-3.94780.25361200.1978268999
3.9478-27.5160.25541510.21532677100

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