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- PDB-5nzd: The structure of the thermobifida fusca guanidine III riboswitch ... -

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Basic information

Entry
Database: PDB / ID: 5nzd
TitleThe structure of the thermobifida fusca guanidine III riboswitch in space group P212121.
Componentsguanidine III riboswitch
KeywordsRNA / guanidine III riboswitch / stem-loop / pseudoknot / gene regulation
Function / homologyACETATE ION / RNA / RNA (> 10)
Function and homology information
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.007 Å
AuthorsHuang, L. / Wang, J. / Lilley, D.M.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKprogram grant A18604 United Kingdom
CitationJournal: Cell Chem Biol / Year: 2017
Title: Structure of the Guanidine III Riboswitch.
Authors: Huang, L. / Wang, J. / Wilson, T.J. / Lilley, D.M.J.
History
DepositionMay 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: guanidine III riboswitch
B: guanidine III riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,30415
Polymers26,9222
Non-polymers38313
Water43224
1
A: guanidine III riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6879
Polymers13,4611
Non-polymers2278
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: guanidine III riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6176
Polymers13,4611
Non-polymers1565
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.460, 64.613, 84.292
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain guanidine III riboswitch


Mass: 13460.812 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermobifida fusca (bacteria)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M Magnesium acetate, 0.05 M MES pH 5.6, 20% v/v 2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.92019 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92019 Å / Relative weight: 1
ReflectionResolution: 2.007→42.146 Å / Num. obs: 33860 / % possible obs: 99.8 % / Observed criterion σ(I): 1.4 / Redundancy: 5.12 % / CC1/2: 0.9848 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.025 / Net I/σ(I): 11.17
Reflection shellResolution: 2.007→2.04 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.282 / Num. unique obs: 882 / CC1/2: 0.816 / Rpim(I) all: 0.623 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(dev_2219: ???)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.007→42.146 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.62
RfactorNum. reflection% reflection
Rfree0.245 1635 4.83 %
Rwork0.22 --
obs0.2213 33860 97.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.007→42.146 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1770 19 24 1813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051986
X-RAY DIFFRACTIONf_angle_d1.5873102
X-RAY DIFFRACTIONf_dihedral_angle_d14.222944
X-RAY DIFFRACTIONf_chiral_restr0.044404
X-RAY DIFFRACTIONf_plane_restr0.00884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0073-2.06640.47061230.45862603X-RAY DIFFRACTION94
2.0664-2.13310.43921370.43612646X-RAY DIFFRACTION95
2.1331-2.20930.4231140.41082694X-RAY DIFFRACTION97
2.2093-2.29780.41591370.37842654X-RAY DIFFRACTION97
2.2978-2.40230.40951640.36632701X-RAY DIFFRACTION98
2.4023-2.5290.40081430.33672680X-RAY DIFFRACTION98
2.529-2.68740.39811340.31472725X-RAY DIFFRACTION98
2.6874-2.89480.33921300.29252760X-RAY DIFFRACTION99
2.8948-3.18610.28491210.23922676X-RAY DIFFRACTION98
3.1861-3.64690.23521520.17342642X-RAY DIFFRACTION95
3.6469-4.59380.17971230.14992744X-RAY DIFFRACTION99
4.5938-42.15520.16071570.15782700X-RAY DIFFRACTION98
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)
10.45850.43271.9380.33121.46367.21180.1768-0.08840.002-0.1040.1593-0.1224-0.38610.3068-0.32980.6354-0.02030.02550.7839-0.02070.357720.97636.6042-1.2909
29.1571-1.45756.94371.47580.43157.4355-0.4258-0.2025-1.35230.69860.88910.002-0.13760.2126-0.40270.8633-0.029-0.03220.62360.07450.518621.148-2.2682-9.9701
31.9775-0.679-0.88582.5036-0.62882.40360.39950.32280.0242-0.3695-0.2482-0.2042-0.66390.908-0.10710.7364-0.0261-0.08631.1722-0.06790.369425.105710.32065.9646
43.23370.7207-1.0833.2775-1.62338.57660.3170.0482-0.0137-0.10780.19270.23440.0634-0.1136-0.45540.46270.0176-0.06930.6447-0.00580.314625.8755-21.4894-2.4281
55.4177-0.4584-2.58355.36320.49029.20550.22550.130.14350.03030.27020.3656-0.9767-0.9816-0.48990.59020.21480.00190.82930.0330.325625.1291-18.943211.9392
64.6715-1.34160.31723.9883-0.59057.55580.23790.38020.3039-1.06830.1905-0.0187-0.1975-0.329-0.43390.69410.0154-0.03640.4977-0.01160.329927.3195-20.4435-13.7478
79.08470.1055-6.22510.25460.06524.29520.14831.1341.0672-0.82410.4892-0.0466-0.6166-1.0136-0.51890.82010.10440.08340.84670.070.47521.249-13.9455-12.9373
82.8648-0.92594.44559.654-1.76697.04220.3168-0.0501-0.43830.12570.43930.87610.6391-1.3495-0.77250.4948-0.0523-0.01740.70990.14670.410217.7817-26.1883-3.58
95.93171.21143.65286.97714.88975.48810.0931-0.179-0.4450.22970.1955-0.00590.6630.1971-0.35780.4802-0.0287-0.04130.63730.08140.28331.9722-24.822210.5379
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 31 )
3X-RAY DIFFRACTION3chain 'A' and (resid 32 through 41 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 11 )
5X-RAY DIFFRACTION5chain 'B' and (resid 12 through 16 )
6X-RAY DIFFRACTION6chain 'B' and (resid 17 through 26 )
7X-RAY DIFFRACTION7chain 'B' and (resid 27 through 31 )
8X-RAY DIFFRACTION8chain 'B' and (resid 32 through 36 )
9X-RAY DIFFRACTION9chain 'B' and (resid 37 through 41 )

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