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- PDB-6p2h: Structural basis for 2'-deoxyguanosine recognition by the 2'-dG-I... -

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Basic information

Entry
Database: PDB / ID: 6p2h
TitleStructural basis for 2'-deoxyguanosine recognition by the 2'-dG-II class of riboswitches
ComponentsRNA (69-MER)
KeywordsRNA / riboswitch aptamer 2'-deoxyguanosine purine nucleoside
Function / homology2'-DEOXY-GUANOSINE / COBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.803 Å
AuthorsMatyjasik, M.M. / Batey, R.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM073850 United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural basis for 2'-deoxyguanosine recognition by the 2'-dG-II class of riboswitches.
Authors: Matyjasik, M.M. / Batey, R.T.
History
DepositionMay 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (69-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,51812
Polymers22,3231
Non-polymers1,19411
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.805, 91.805, 77.756
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+3/4
#8: -y,-x,-z+1/4
Components on special symmetry positions
IDModelComponents
11A-207-

HOH

21A-212-

HOH

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Components

#1: RNA chain RNA (69-MER) / Env1 2'-deoxyguanosine-II riboswitch aptamer domain


Mass: 22323.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-GNG / 2'-DEOXY-GUANOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CoH18N6
#4: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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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: 3.67 Å3/Da / Density % sol: 66.48 % / Description: Tetragonal
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 40 mM sodium cacodylate pH 6.0, 23% v/v methylpentanediol, 18 mM cobalt hexamine, 80 mM potassium chloride, and 12 mM sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen cryostream / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 22, 2018
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.803→29.953 Å / Num. obs: 8547 / % possible obs: 97.69 % / Redundancy: 10.8 % / Biso Wilson estimate: 58.19 Å2 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.03 / Χ2: 1.99 / Net I/σ(I): 27.25
Reflection shellResolution: 2.803→2.904 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 3.37 / Num. unique obs: 816 / CC1/2: 0.946 / Rpim(I) all: 0.195 / Χ2: 1.515 / % possible all: 97.69

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Processing

Software
NameVersionClassification
PHENIX1.14-3260refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FE5

4fe5


Resolution: 2.803→29.953 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30
RfactorNum. reflection% reflection
Rfree0.2756 843 10 %
Rwork0.2443 --
obs0.2474 8547 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.803→29.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1478 59 12 1549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011704
X-RAY DIFFRACTIONf_angle_d0.5352675
X-RAY DIFFRACTIONf_dihedral_angle_d14.997827
X-RAY DIFFRACTIONf_chiral_restr0.024347
X-RAY DIFFRACTIONf_plane_restr0.00270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8035-2.9790.49741350.42131221X-RAY DIFFRACTION98
2.979-3.20880.35181320.31871220X-RAY DIFFRACTION97
3.2088-3.53120.30941400.26541243X-RAY DIFFRACTION98
3.5312-4.04110.25681400.22371246X-RAY DIFFRACTION98
4.0411-5.08730.23511440.20421278X-RAY DIFFRACTION99
5.0873-29.95470.24081520.22171383X-RAY DIFFRACTION99

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