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- PDB-5ndh: The structure of the G. violaceus guanidine II riboswitch P2 stem-loop -

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Basic information

Entry
Database: PDB / ID: 5ndh
TitleThe structure of the G. violaceus guanidine II riboswitch P2 stem-loop
ComponentsRNA (5'-R(*GP*(CBV)P*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*GP*C)-3')
KeywordsRNA / guanidine II riboswitch / stem-loop / tetra loop / dimer
Function / homologyGUANIDINE / RNA / RNA (> 10)
Function and homology information
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.81 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 8, 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 1.3May 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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,52515
Polymers20,9804
Non-polymers54511
Water1,45981
1
A: RNA (5'-R(*GP*(CBV)P*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*GP*C)-3')
C: RNA (5'-R(*GP*(CBV)P*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6797
Polymers10,4902
Non-polymers1885
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (5'-R(*GP*(CBV)P*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*GP*C)-3')
D: RNA (5'-R(*GP*(CBV)P*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8468
Polymers10,4902
Non-polymers3566
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.727, 57.825, 100.862
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain , 1 types, 4 molecules ABCD

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


Mass: 5245.062 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Gloeobacter violaceus (bacteria)

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Non-polymers , 5 types, 92 molecules

#2: Chemical
ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH5N3
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 3.39 Å3/Da / Density % sol: 63.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.01 M Magnesium Sulfate, 0.05 M Sodium Cacodylate pH 6.0, 1.8 M Lithium Sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92011 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92011 Å / Relative weight: 1
ReflectionResolution: 1.81→50.17 Å / Num. obs: 49436 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 34.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.026 / Net I/σ(I): 16.2
Reflection shellResolution: 1.81→1.84 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.41 / Mean I/σ(I) obs: 1.1 / Num. unique all: 1275 / CC1/2: 0.55 / Rpim(I) all: 0.66 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(dev_2219: ???)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.81→50.166 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.4
RfactorNum. reflection% reflection
Rfree0.2222 2455 4.97 %
Rwork0.2066 --
obs0.2075 49436 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.81→50.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1376 31 81 1488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051556
X-RAY DIFFRACTIONf_angle_d2.0552424
X-RAY DIFFRACTIONf_dihedral_angle_d10.451720
X-RAY DIFFRACTIONf_chiral_restr0.039312
X-RAY DIFFRACTIONf_plane_restr0.00668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.84480.38691270.41852379X-RAY DIFFRACTION90
1.8448-1.88240.40111090.39892533X-RAY DIFFRACTION95
1.8824-1.92340.40131270.38072571X-RAY DIFFRACTION96
1.9234-1.96810.39131290.37392622X-RAY DIFFRACTION98
1.9681-2.01730.35041330.36562597X-RAY DIFFRACTION99
2.0173-2.07190.36021500.32642615X-RAY DIFFRACTION99
2.0719-2.13290.31761310.30942635X-RAY DIFFRACTION99
2.1329-2.20170.2941270.28522666X-RAY DIFFRACTION100
2.2017-2.28040.31541440.27722624X-RAY DIFFRACTION100
2.2804-2.37170.27411340.25832647X-RAY DIFFRACTION100
2.3717-2.47960.26631280.25572632X-RAY DIFFRACTION100
2.4796-2.61040.27741560.24312654X-RAY DIFFRACTION100
2.6104-2.77390.29971210.24062646X-RAY DIFFRACTION100
2.7739-2.9880.23911410.22052646X-RAY DIFFRACTION100
2.988-3.28870.18371440.18312619X-RAY DIFFRACTION99
3.2887-3.76440.14081320.15342652X-RAY DIFFRACTION100
3.7644-4.74220.17391460.14932646X-RAY DIFFRACTION100
4.7422-50.18490.19141760.15142597X-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)
10.57620.7111-0.20526.68580.56380.2316-0.0023-0.01310.1387-0.2399-0.1042-0.3906-0.0548-0.03220.12490.3149-0.0475-0.04080.33740.04510.369515.191246.138313.8955
24.16390.3001-0.35241.04940.30860.6855-0.0139-0.18530.15030.14-0.0287-0.0986-0.0280.0371-0.00380.3744-0.0505-0.06250.30820.01830.33525.26225.174111.715
31.3433-0.1284-0.05522.98691.36532.70380.1026-0.03570.038-0.31380.00180.0423-0.1226-0.1911-0.16370.3901-0.0491-0.00630.28020.04590.250714.62325.5323.0236
42.28-0.2884-1.14881.3227-0.48213.84470.0079-0.2186-0.1423-0.07530.12520.0106-0.00570.17-0.1160.3491-0.071-0.05780.40580.01390.296-15.14312.183822.3261
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 16 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 16 )
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 16 )

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