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- PDB-6cb3: Crystal structure of the L.Lactis YkoY riboswitch bound to cadmium -

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Basic information

Entry
Database: PDB / ID: 6cb3
TitleCrystal structure of the L.Lactis YkoY riboswitch bound to cadmium
ComponentsRNA (99-MER)
KeywordsRNA / Riboswitch / Cadmium / yybP-ykoY
Function / homology: / : / GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.891 Å
AuthorsBachas, S. / Ferre-D'amare, A.R.
CitationJournal: Cell Chem Biol / Year: 2018
Title: Convergent Use of Heptacoordination for Cation Selectivity by RNA and Protein Metalloregulators.
Authors: Bachas, S.T. / Ferre-D'Amare, A.R.
History
DepositionFeb 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3Oct 4, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 (99-MER)
B: RNA (99-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,54861
Polymers65,2992
Non-polymers7,24959
Water6,179343
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.141, 73.141, 117.610
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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RNA chain , 1 types, 2 molecules AB

#1: RNA chain RNA (99-MER)


Mass: 32649.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Lactococcus lactis (lactic acid bacteria)

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Non-polymers , 5 types, 402 molecules

#2: Chemical...
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Ba
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.84 Å3/Da / Density % sol: 56.66 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 40 mM Sodium Cacodylate pH 7.0, 80 mM NaCl, 20 mM BaCl2, 5 mM CdCl2, 12 mM spermine hydrochloride, 12% 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.988 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 56296 / % possible obs: 99 % / Redundancy: 5.5 % / Net I/σ(I): 57.98
Reflection shellResolution: 1.89→1.92 Å

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4y1i

4y1i


Resolution: 1.891→43.096 Å / Cross valid method: FREE R-VALUE / σ(F): 4.6 / Phase error: 36.4
RfactorNum. reflection% reflection
Rfree0.1737 3133 5.57 %
Rwork0.14 --
obs0.1468 56199 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.891→43.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4244 121 343 4708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134822
X-RAY DIFFRACTIONf_angle_d1.6567516
X-RAY DIFFRACTIONf_dihedral_angle_d13.2642398
X-RAY DIFFRACTIONf_chiral_restr0.074998
X-RAY DIFFRACTIONf_plane_restr0.01200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8918-1.92440.29331650.25722709X-RAY DIFFRACTION94
1.9244-1.95940.25421350.24992606X-RAY DIFFRACTION95
1.9594-1.99710.26971580.24662654X-RAY DIFFRACTION94
1.9971-2.03780.26561610.23522710X-RAY DIFFRACTION94
2.0378-2.08210.27961480.22912624X-RAY DIFFRACTION95
2.0821-2.13060.27891710.21972674X-RAY DIFFRACTION94
2.1306-2.18380.27391790.21962589X-RAY DIFFRACTION94
2.1838-2.24290.22781510.20932640X-RAY DIFFRACTION95
2.2429-2.30890.25922110.20482646X-RAY DIFFRACTION93
2.3089-2.38340.25441540.19412641X-RAY DIFFRACTION94
2.3834-2.46850.26221450.1912668X-RAY DIFFRACTION95
2.4685-2.56740.22271420.18682623X-RAY DIFFRACTION95
2.5674-2.68420.24441550.18462682X-RAY DIFFRACTION95
2.6842-2.82560.22051510.17482688X-RAY DIFFRACTION95
2.8256-3.00260.18841380.15492622X-RAY DIFFRACTION95
3.0026-3.23430.15831330.13582695X-RAY DIFFRACTION95
3.2343-3.55950.15141890.12552615X-RAY DIFFRACTION93
3.5595-4.0740.12591490.10462679X-RAY DIFFRACTION95
4.074-5.13060.12141470.09422651X-RAY DIFFRACTION95
5.1306-36.57730.13931510.09712637X-RAY DIFFRACTION94
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)
11.1671-0.4010.03630.78540.24361.0546-0.05390.05940.00230.00880.00840.0902-0.02-0.23360.03640.1919-0.0259-0.02230.37090.00630.17949.60513.4458-11.1251
20.7491-0.15921.36280.206-0.30692.4423-0.0479-0.0524-0.0036-0.00120.1528-0.0396-0.01030.13-0.1150.25110.0048-0.04480.5336-0.03510.2507-4.70027.6756-19.626
30.7777-0.35490.12850.7892-0.19030.5098-0.0470.0316-0.02370.1427-0.0143-0.0309-0.02260.05850.05790.36910.084-0.00630.25050.04060.209532.9447-10.211326.8477
40.6419-0.21421.12170.1994-0.51182.39350.12520.06070.0090.0163-0.05340.00570.00670.0479-0.06750.33120.0702-0.00050.28060.04460.255144.9612-19.318833.9668
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:68 )A3 - 68
2X-RAY DIFFRACTION2( CHAIN A AND RESID 69:100 )A69 - 100
3X-RAY DIFFRACTION3( CHAIN B AND RESID 3:70 )B3 - 70
4X-RAY DIFFRACTION4( CHAIN B AND RESID 71:100 )B71 - 100

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