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- PDB-4y1j: Lactococcus lactis yybP-ykoY Mn riboswitch A41U binding site muta... -

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Basic information

Entry
Database: PDB / ID: 4y1j
TitleLactococcus lactis yybP-ykoY Mn riboswitch A41U binding site mutant in presence of Mn2+
ComponentsyybP-ykoY riboswitch
KeywordsRNA / riboswitch / manganese-binding / mutant
Function / homologyGUANOSINE-5'-TRIPHOSPHATE / STRONTIUM ION / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.24 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 7, 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_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.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

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Assembly

Deposited unit
A: yybP-ykoY riboswitch
B: yybP-ykoY riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,74880
Polymers64,5622
Non-polymers6,18678
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16120 Å2
ΔGint-2064 kcal/mol
Surface area31330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.419, 62.510, 69.969
Angle α, β, γ (deg.)116.21, 101.83, 98.83
Int Tables number1
Space group name H-MP1

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Components

#1: RNA chain yybP-ykoY riboswitch


Mass: 32281.215 Da / Num. of mol.: 2 / Mutation: A41U / Source method: obtained synthetically
Source: (synth.) Lactococcus lactis subsp. lactis (lactic acid bacteria)
#2: 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
#3: Chemical...
ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 52 / Source method: obtained synthetically / Formula: Sr
#4: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.88 Å3/Da / Density % sol: 57.31 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1-0.2 mM RNA in 10 mM Na Cacodylate pH 7, 50 mM NaCl, 10 mM MgCl2, 2.5 mM MnCl2. Crystallized in about 2 months with a mother liquor of 40 mM Na cacodylate pH 6, 15% MPD, 80 mM SrCl2, 12 ...Details: 0.1-0.2 mM RNA in 10 mM Na Cacodylate pH 7, 50 mM NaCl, 10 mM MgCl2, 2.5 mM MnCl2. Crystallized in about 2 months with a mother liquor of 40 mM Na cacodylate pH 6, 15% MPD, 80 mM SrCl2, 12 mM spermine tetra-HCl at 21 C. Crystals were cryo-protected by addition of 20% PEG-400 directly before freezing.

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.769 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.769 Å / Relative weight: 1
ReflectionResolution: 2.24→47.4 Å / Num. obs: 32334 / % possible obs: 90 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 17.6
Reflection shellResolution: 2.24→2.32 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.1 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1555)refinement
XDSdata reduction
Aimlessdata scaling
PHENIX(phenix.refine: dev_1555)phasing
RefinementMethod to determine structure: SAD / Resolution: 2.24→47.4 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0.44 / Phase error: 32.71 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2415 1742 5.55 %
Rwork0.1993 --
obs0.2017 29646 89.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.24→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4280 140 209 4629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054860
X-RAY DIFFRACTIONf_angle_d1.0387574
X-RAY DIFFRACTIONf_dihedral_angle_d15.7592420
X-RAY DIFFRACTIONf_chiral_restr0.0441008
X-RAY DIFFRACTIONf_plane_restr0.007202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.33010.40251350.32732319X-RAY DIFFRACTION88
2.4-2.49130.38431400.3022374X-RAY DIFFRACTION90
2.4913-2.5910.42641360.31412369X-RAY DIFFRACTION90
2.591-2.70890.33671320.31252262X-RAY DIFFRACTION86
2.7089-2.85170.33691470.29382460X-RAY DIFFRACTION92
2.8517-3.03040.29311450.25512460X-RAY DIFFRACTION94
3.0304-3.26440.27741440.21872453X-RAY DIFFRACTION93
3.2644-3.59280.22661360.19482310X-RAY DIFFRACTION87
3.5928-4.11260.20741480.16132523X-RAY DIFFRACTION95
4.1126-5.18080.18421400.15122384X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: -39.1649 Å / Origin y: -10.1398 Å / Origin z: 10.1027 Å
111213212223313233
T0.3538 Å20.0131 Å2-0.0083 Å2-0.3705 Å2-0.0204 Å2--0.4491 Å2
L0.5846 °20.0911 °2-0.0448 °2-0.1431 °2-0.0559 °2--0.5529 °2
S-0.0243 Å °0.0063 Å °-0.0657 Å °-0.0363 Å °0.0136 Å °0.0057 Å °0.0459 Å °-0.0519 Å °-0.0003 Å °
Refinement TLS groupSelection details: all

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