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- PDB-5nex: The structure of the G. violaceus guanidine II riboswitch P1 stem... -

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Basic information

Entry
Database: PDB / ID: 5nex
TitleThe structure of the G. violaceus guanidine II riboswitch P1 stem-loop with agmatine
ComponentsRNA (5'-R(*GP*GP*UP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*AP*(CBV)P*C)-3')
KeywordsRNA / guanidine II riboswitch / stem-loop / tetra loop / dimer / agmatine
Function / homologyAGMATINE / RNA / RNA (> 10)
Function and homology information
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.72 Å
AuthorsHuang, L. / Wang, J. / Lilley, D.M.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
CitationJournal: Cell Chem Biol / Year: 2017
Title: The Structure of the Guanidine-II Riboswitch.
Authors: Huang, L. / Wang, J. / Lilley, D.M.J.
History
DepositionMar 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 20, 2019Group: Data collection / Derived calculations / Structure summary
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _struct_keywords.text
Revision 1.4May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*GP*GP*UP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*AP*(CBV)P*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,19510
Polymers5,8801
Non-polymers3149
Water27015
1
A: RNA (5'-R(*GP*GP*UP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*AP*(CBV)P*C)-3')
hetero molecules

A: RNA (5'-R(*GP*GP*UP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*AP*(CBV)P*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,38920
Polymers11,7612
Non-polymers62818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
Unit cell
Length a, b, c (Å)55.639, 55.639, 135.927
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-102-

NA

21A-103-

NA

31A-105-

NA

41A-106-

NA

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Components

#1: RNA chain RNA (5'-R(*GP*GP*UP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*AP*(CBV)P*C)-3')


Mass: 5880.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Gloeobacter violaceus (bacteria)
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-AG2 / AGMATINE / (4-AMINOBUTYL)GUANIDINE


Mass: 130.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H14N4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.44 Å3/Da / Density % sol: 64.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.01 M Magnesium Acetate, 0.05 M MES pH 5.6, 2.5 M Ammonium Sulfate soaking with 500mM agmatine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9179 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 1.719→45.42 Å / Num. obs: 16643 / % possible obs: 100 % / Observed criterion σ(I): 1.4 / Redundancy: 18.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.031 / Net I/σ(I): 10.7
Reflection shellResolution: 1.719→1.75 Å / Redundancy: 17.8 % / Rmerge(I) obs: 1.5 / Num. unique obs: 452 / CC1/2: 0.752 / Rpim(I) all: 0.948 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(dev_2219: ???)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.72→45.416 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.4
RfactorNum. reflection% reflection
Rfree0.2331 930 5.59 %
Rwork0.2005 --
obs0.2022 16643 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.72→45.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 386 17 15 418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008447
X-RAY DIFFRACTIONf_angle_d1.383689
X-RAY DIFFRACTIONf_dihedral_angle_d11.776212
X-RAY DIFFRACTIONf_chiral_restr0.04488
X-RAY DIFFRACTIONf_plane_restr0.00920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7193-1.80990.32761350.31592237X-RAY DIFFRACTION99
1.8099-1.92330.29881290.29532267X-RAY DIFFRACTION100
1.9233-2.07180.27951150.25322272X-RAY DIFFRACTION100
2.0718-2.28030.281330.21482209X-RAY DIFFRACTION100
2.2803-2.61030.26571510.21862248X-RAY DIFFRACTION100
2.6103-3.28850.24171690.2152202X-RAY DIFFRACTION99
3.2885-45.43140.1735980.16052278X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1994-0.1740.81094.063-3.92285.26280.0767-0.0330.03510.30860.07470.0064-0.34260.2446-0.06920.3151-0.0240.0130.3064-0.04510.267-18.250721.011415.3231
26.9485-2.63522.96954.4847-4.31416.8891-0.13220.19490.18440.1366-0.115-0.2827-0.43730.69720.19790.233-0.01970.01170.2951-0.00310.2368-16.178718.30169.1254
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 18 )

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