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- PDB-7d7z: Crystal Structure of the Domain1 of NAD+ Riboswitch with nicotina... -

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Basic information

Entry
Database: PDB / ID: 7d7z
TitleCrystal Structure of the Domain1 of NAD+ Riboswitch with nicotinamide adenine dinucleotide (NAD+), soaked in Mn2+
Components18GAAA(52-MER)
KeywordsRNA / riboswitch / RNA structure / RNA folding / RNA-ligand interactions / RNA crystallography
Function / homologyGUANOSINE-5'-TRIPHOSPHATE / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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: 18GAAA(52-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,77230
Polymers16,4391
Non-polymers2,33329
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.804, 57.318, 196.564
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-124-

MN

21A-252-

HOH

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain 18GAAA(52-MER)


Mass: 16438.873 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 121 molecules

#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NAD / 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.78 Å3/Da / Density % sol: 74.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.5, 1.6 M MgSO4

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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: 2.59→30 Å / Num. obs: 18682 / % possible obs: 99.7 % / Redundancy: 13 % / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.04 / Rrim(I) all: 0.146 / Χ2: 0.645 / Net I/σ(I): 3.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.6913.71.4629850.8070.4071.5190.418100
2.69-2.813.70.929980.9290.2560.9550.406100
2.8-2.9313.50.69950.9780.1680.6230.418100
2.93-3.0813.30.2619960.9960.0740.2720.454100
3.08-3.28130.1689890.9980.0480.1750.519100
3.28-3.5311.60.12810110.9980.0390.1340.5999.2
3.53-3.88130.1229980.9970.0350.1270.68299.8
3.88-4.4413.50.11110330.9960.0310.1150.82299.7
4.44-5.59130.10310220.9950.0290.1070.95699.5
5.59-30120.10310840.9960.0310.1071.19298.6

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Processing

Software
NameVersionClassification
PHENIXv1.14refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D7V

7d7v


Resolution: 2.6→30 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.244 881 -
Rwork0.213 --
obs-10067 99.22 %
Displacement parametersBiso max: 125.69 Å2 / Biso mean: 58.8634 Å2 / Biso min: 37.51 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1123 71 92 1286
LS refinement shellResolution: 2.6→2.7588 Å /
RfactorNum. reflection
Rfree0.4956 150
Rwork0.4226 -

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