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- PDB-5nz3: The structure of the thermobifida fusca guanidine III riboswitch ... -

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Basic information

Entry
Database: PDB / ID: 5nz3
TitleThe structure of the thermobifida fusca guanidine III riboswitch with methylguanidine
ComponentsRNA (41-MER)
KeywordsRNA / guanidine III riboswitch / stem-loop / pseudoknot / gene regulation
Function / homology1-METHYLGUANIDINE / RNA / RNA (> 10)
Function and homology information
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.059 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 12, 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 1.2Oct 16, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_CC_half
Revision 1.3May 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
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_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: RNA (41-MER)
B: RNA (41-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,20812
Polymers26,9222
Non-polymers28710
Water39622
1
A: RNA (41-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6768
Polymers13,4611
Non-polymers2157
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA (41-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5324
Polymers13,4611
Non-polymers723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.491, 83.491, 66.071
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: RNA chain RNA (41-MER)


Mass: 13460.812 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermobifida fusca (bacteria)
#2: Chemical ChemComp-MGX / 1-METHYLGUANIDINE


Mass: 73.097 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7N3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.47 Å3/Da / Density % sol: 50.19 %
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: 2.059→48.775 Å / Num. obs: 31161 / % possible obs: 99.9 % / Observed criterion σ(I): 1.2 / Redundancy: 15.07 % / CC1/2: 1 / Rmerge(I) obs: 0.1061 / Rpim(I) all: 0.028 / Net I/σ(I): 11.15
Reflection shellResolution: 2.06→2.09 Å / Redundancy: 14.5 % / Rmerge(I) obs: 2.233 / Num. unique obs: 788 / CC1/2: 0.723 / Rpim(I) all: 0.603 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX(dev_2219: ???)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.059→48.775 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.9
RfactorNum. reflection% reflection
Rfree0.2737 1572 5.04 %
Rwork0.2185 --
obs0.221 31161 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.059→48.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1770 14 22 1806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071984
X-RAY DIFFRACTIONf_angle_d1.4393100
X-RAY DIFFRACTIONf_dihedral_angle_d12.956944
X-RAY DIFFRACTIONf_chiral_restr0.062404
X-RAY DIFFRACTIONf_plane_restr0.01183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0593-2.12580.40521410.39322650X-RAY DIFFRACTION96
2.1258-2.20180.38521650.37382661X-RAY DIFFRACTION98
2.2018-2.28990.43531480.37622620X-RAY DIFFRACTION97
2.2899-2.39420.41791310.33512706X-RAY DIFFRACTION97
2.3942-2.52040.37781750.33192619X-RAY DIFFRACTION97
2.5204-2.67830.3351510.33042656X-RAY DIFFRACTION97
2.6783-2.8850.37811340.29922749X-RAY DIFFRACTION98
2.885-3.17530.27621330.21722632X-RAY DIFFRACTION98
3.1753-3.63470.22791120.15872795X-RAY DIFFRACTION99
3.6347-4.57880.20391210.17312746X-RAY DIFFRACTION100
4.5788-48.78840.22251610.17122755X-RAY DIFFRACTION100
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)
12.70673.84833.73575.50665.40628.38440.0078-0.4181-0.50670.4475-0.2415-0.06560.66340.5279-0.02120.3050.00240.05150.69670.04140.2971-23.526627.0947-6.8974
21.47030.24710.25080.7575-0.24550.7783-0.0535-0.0516-0.2849-0.02780.0432-0.2440.12790.06460.03170.3114-0.04220.01950.46670.00030.237-36.014123.0502-13.0495
31.33980.1555-0.03580.36340.07821.0953-0.24570.1068-0.2277-0.0380.1066-0.17360.0857-0.01720.0950.3231-0.04390.03240.38540.00880.2722-34.050423.7995-13.9943
40.84540.1410.71771.65290.91160.97340.0962-0.30580.5772-0.2678-0.31210.02960.06770.21030.1226-0.0493-0.01380.49441.66690.57081.5808-47.43652.2996-18.3132
51.1678-0.5447-0.35660.2640.16980.0143-0.05670.30960.85360.55550.18671.29-0.108-0.32480.0980.2560.09360.09411.04050.19011.3326-35.461854.2518-11.5484
61.2943-0.7578-0.81110.70870.61920.82080.17010.26831.17570.061-0.04521.4845-0.3044-1.12770.0250.44410.24610.07031.28090.03031.8212-37.350555.5865-11.6398
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 5 )
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 25 )
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 41 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 5 )
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 25 )
6X-RAY DIFFRACTION6chain 'B' and (resid 26 through 41 )

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