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- PDB-6cc1: Crystal structure of ykoY-alx riboswitch chimera bound to cadmium -

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Basic information

Entry
Database: PDB / ID: 6cc1
TitleCrystal structure of ykoY-alx riboswitch chimera bound to cadmium
ComponentsRNA (94-MER)
KeywordsRNA / Riboswich / 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 / Resolution: 2.54 Å
AuthorsBachas, S.T. / 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 5, 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
Revision 1.2Mar 13, 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_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.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.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.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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (94-MER)
B: RNA (94-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,05436
Polymers65,2992
Non-polymers4,75534
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-234 kcal/mol
Surface area32530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.089, 73.089, 117.082
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 (94-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, 117 molecules

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


Mass: 112.411 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ba
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 40 mM Sodium Cacodylate, 80mM Sodium Chloride, 20 mM Barium Chloride, 5 mM Cadium Chloride, 12mM sprimine tetrahydrochloride, 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: 0.99 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 29350 / % possible obs: 99 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.056 / Rrim(I) all: 0.112 / Net I/σ(I): 33.99
Reflection shellResolution: 2.35→2.39 Å / Rmerge(I) obs: 1 / Num. unique obs: 1358

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.54→42.978 Å / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 32.54
RfactorNum. reflection% reflection
Rfree0.281 1554 6.78 %
Rwork0.2219 --
obs0.2288 22931 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.54→42.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4126 96 83 4305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024690
X-RAY DIFFRACTIONf_angle_d0.6667306
X-RAY DIFFRACTIONf_dihedral_angle_d15.3312325
X-RAY DIFFRACTIONf_chiral_restr0.029968
X-RAY DIFFRACTIONf_plane_restr0.004194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5435-2.62550.49371560.42631972X-RAY DIFFRACTION93
2.6255-2.71930.37671400.40051935X-RAY DIFFRACTION93
2.7193-2.8280.44111380.38251961X-RAY DIFFRACTION93
2.828-2.95650.39091380.33011915X-RAY DIFFRACTION93
2.9565-3.11210.33741400.30221949X-RAY DIFFRACTION93
3.1121-3.30660.27121440.27991960X-RAY DIFFRACTION93
3.3066-3.56120.28161440.25171924X-RAY DIFFRACTION93
3.5612-3.91830.25291490.22661956X-RAY DIFFRACTION93
3.9183-4.48230.23661250.19291946X-RAY DIFFRACTION94
4.4823-5.6360.29641460.18131964X-RAY DIFFRACTION93
5.636-24.58280.23741330.15911840X-RAY DIFFRACTION89

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