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- PDB-4y1m: An Escherichia coli yybP-ykoY Mn riboswitch in the Mn2+-free state -

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Basic information

Entry
Database: PDB / ID: 4y1m
TitleAn Escherichia coli yybP-ykoY Mn riboswitch in the Mn2+-free state
ComponentsE. coli yybP-ykoY riboswitch
KeywordsRNA / riboswitch / manganese / free state
Function / homologyGUANOSINE-5'-TRIPHOSPHATE / STRONTIUM ION / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsPrice, I.R. / Ke, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM086766 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 102543 United States
CitationJournal: Mol.Cell / Year: 2015
Title: Mn(2+)-Sensing Mechanisms of yybP-ykoY Orphan Riboswitches.
Authors: Price, I.R. / Gaballa, A. / Ding, F. / Helmann, J.D. / Ke, A.
History
DepositionFeb 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Data collection
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 28, 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
B: E. coli yybP-ykoY riboswitch
A: E. coli yybP-ykoY riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,13678
Polymers69,1752
Non-polymers6,96076
Water1,29772
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B: E. coli yybP-ykoY riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,00050
Polymers34,5881
Non-polymers4,41249
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: E. coli yybP-ykoY riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,13628
Polymers34,5881
Non-polymers2,54827
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)159.384, 159.384, 277.108
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-231-

SR

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Components

#1: RNA chain E. coli yybP-ykoY riboswitch


Mass: 34587.578 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#2: Chemical...
ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 65 / Source method: obtained synthetically / Formula: Sr
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.83 Å3/Da / Density % sol: 74.52 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.2 mM RNA in 10 mm NaCacodylate, 50 mM NaCl, 10 mM MgCl2 with a mother liquor of 10% MPD, 40 mM Na cacodylate pH 7, 80 mM SrCl2, 20 mM MgCl2, 12 mM spermine tetra-HCl at 21 C. Native ...Details: 0.2 mM RNA in 10 mm NaCacodylate, 50 mM NaCl, 10 mM MgCl2 with a mother liquor of 10% MPD, 40 mM Na cacodylate pH 7, 80 mM SrCl2, 20 mM MgCl2, 12 mM spermine tetra-HCl at 21 C. Native crystals were quickly cryo-protected in mother liquor plus 20% ethylene glycol prior to flash freezing in liquid N2.

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.769, 0.7692, 0.9999
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.7691
20.76921
30.99991
ReflectionResolution: 3→123.6 Å / Num. obs: 27410 / % possible obs: 100 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 20.2
Reflection shellResolution: 3→3.11 Å / Redundancy: 11.6 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 2.41 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1834)refinement
XDSdata reduction
Aimlessdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 3→123.6 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2521 1623 6.38 %
Rwork0.2166 --
obs0.2186 26818 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→123.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3916 138 72 4126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024507
X-RAY DIFFRACTIONf_angle_d0.6146927
X-RAY DIFFRACTIONf_dihedral_angle_d17.052260
X-RAY DIFFRACTIONf_chiral_restr0.067915
X-RAY DIFFRACTIONf_plane_restr0.002185
Refinement TLS params.Method: refined / Origin x: 32.5983 Å / Origin y: 2.9323 Å / Origin z: 29.2014 Å
111213212223313233
T0.6173 Å2-0.0054 Å2-0.1154 Å2-0.9284 Å20.0239 Å2--0.596 Å2
L2.1825 °20.045 °2-1.2918 °2-0.8111 °20.5984 °2--3.7202 °2
S-0.1791 Å °-0.1282 Å °-0.3088 Å °0.0667 Å °0.0788 Å °-0.1376 Å °0.3652 Å °0.9194 Å °0.114 Å °
Refinement TLS groupSelection details: all

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