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- PDB-7d7x: Crystal Structure of the Domain1 of NAD+ Riboswitch with adenosin... -

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Basic information

Entry
Database: PDB / ID: 7d7x
TitleCrystal Structure of the Domain1 of NAD+ Riboswitch with adenosine diphosphate (ADP)
Components18GAAA(52-MER)
KeywordsRNA / riboswitch / RNA structure / RNA folding / RNA-ligand interactions / RNA crystallography
Function / homologyADENOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.631 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 / _citation_author.name
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)17,58411
Polymers16,4391
Non-polymers1,14510
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-58 kcal/mol
Surface area9410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.337, 57.400, 196.826
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 16438.873 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine 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.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 4.75 Å3/Da / Density % sol: 74.13 %
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: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.631→50 Å / Num. obs: 9705 / % possible obs: 99.9 % / Redundancy: 12 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.03 / Rrim(I) all: 0.107 / Χ2: 0.773 / Net I/σ(I): 4.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.64-2.739.90.9459430.9040.2890.990.42199.5
2.73-2.8411.10.6079540.9840.1820.6350.416100
2.84-2.9712.20.3299540.9960.0960.3430.422100
2.97-3.1312.30.1859490.9990.0550.1930.479100
3.13-3.3311.80.1299610.9980.0410.1360.521100
3.33-3.5813.50.0959510.9990.0270.0990.582100
3.58-3.9413.40.0859670.9990.0240.0880.73100
3.94-4.5112.60.0889770.9990.0260.0910.965100
4.51-5.6912.10.0839960.9980.0250.0871.361100
5.69-5011.50.07910530.9970.0240.0831.68299.8

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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: 2.631→26.636 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 37.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2427 478 5.04 %
Rwork0.2222 9015 -
obs0.2233 9493 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.72 Å2 / Biso mean: 79.8285 Å2 / Biso min: 57.31 Å2
Refinement stepCycle: final / Resolution: 2.631→26.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1123 35 40 1198
Biso mean--79.16 78.12 -
Num. residues----52
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6311-3.01140.43661640.4088292698
3.0114-3.79220.27841460.2395295497
3.7922-26.6360.19171680.1832313599

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