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- PDB-9jgm: The Escherichia coli yybp riboswitch as a tandem riboswitch regul... -

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Basic information

Entry
Database: PDB / ID: 9jgm
TitleThe Escherichia coli yybp riboswitch as a tandem riboswitch regulated by Mn2+ and pH
ComponentsyybP riboswitch
KeywordsRNA / yybP / riboswitch / conformational dynamics
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.73 Å
AuthorsXiao, W.W. / Liu, G.F. / Chen, T. / Zhang, Y.L. / Ke, A.L. / Cai, R.J. / Lu, C.R.
Funding support China, 2items
OrganizationGrant numberCountry
Other governmentNo. CUSF-DH-D-2019076 China
Other government21YF1433000 China
CitationJournal: Acs Chem.Biol. / Year: 2025
Title: Escherichia coli yybP-ykoY Riboswitch as a Tandem Riboswitch Regulated by Mn 2+ and pH.
Authors: Xiao, W. / Liu, G. / Chen, T. / Zhang, Y. / Ke, A. / Cai, R. / Lu, C.
History
DepositionSep 8, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: yybP riboswitch
A: yybP riboswitch
D: yybP riboswitch
B: yybP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,46833
Polymers135,6414
Non-polymers82729
Water00
1
C: yybP riboswitch
D: yybP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,31920
Polymers67,8202
Non-polymers49918
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-131 kcal/mol
Surface area34320 Å2
MethodPISA
2
B: yybP riboswitch
hetero molecules

A: yybP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,14913
Polymers67,8202
Non-polymers32911
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x+y-1,-x,z-1/31
Buried area2110 Å2
ΔGint-71 kcal/mol
Surface area34280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.416, 144.416, 161.788
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: RNA chain
yybP riboswitch


Mass: 33910.160 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
Has ligand of interestN
Has protein modificationN

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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: 3.59 Å3/Da / Density % sol: 65.74 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: The mother liquor contained 12 mM spermine, 20 mM MgCl2, 15 mM NaCl, 40 mM Na cacodylate pH7.0, 10% 2-methyl-2,4-pentanediol (MPD)

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.24 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 3.73→161.31 Å / Num. obs: 20018 / % possible obs: 100 % / Redundancy: 11 % / CC1/2: 0.997 / Net I/σ(I): 6.5
Reflection shellResolution: 3.73→4.09 Å / Num. unique obs: 101363 / CC1/2: 0.556

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y1I

4y1i


Resolution: 3.73→72.21 Å / SU ML: 0.5323 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 37.5212
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2857 1078 5.41 %
Rwork0.2361 18830 -
obs0.2389 19908 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 196.71 Å2
Refinement stepCycle: LAST / Resolution: 3.73→72.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 8988 29 0 9017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001410056
X-RAY DIFFRACTIONf_angle_d0.423215672
X-RAY DIFFRACTIONf_chiral_restr0.02182100
X-RAY DIFFRACTIONf_plane_restr0.0019420
X-RAY DIFFRACTIONf_dihedral_angle_d15.34345028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.73-3.90.33851270.30052354X-RAY DIFFRACTION99.72
3.9-4.110.31661270.26142359X-RAY DIFFRACTION100
4.11-4.360.2891340.29172363X-RAY DIFFRACTION100
4.36-4.70.33631560.28382325X-RAY DIFFRACTION99.96
4.7-5.170.37441470.3242348X-RAY DIFFRACTION99.92
5.17-5.920.34631350.27992350X-RAY DIFFRACTION100
5.92-7.460.32041230.27232387X-RAY DIFFRACTION100
7.46-72.210.22171290.16582344X-RAY DIFFRACTION97.55
Refinement TLS params.Method: refined / Origin x: -56.306 Å / Origin y: 33.647 Å / Origin z: -32.473 Å
111213212223313233
T1.29912807328 Å2-0.124961393119 Å20.0392998685027 Å2-1.41243643454 Å2-0.102591147021 Å2--1.31491233902 Å2
L-0.113372929477 °2-0.0849450437219 °20.0237332186666 °2--6.64882132643E-5 °2-0.072076765988 °2---0.18878238486 °2
S-0.0393681760073 Å °0.0208253784446 Å °0.107885083593 Å °-0.109249978274 Å °0.00121384131243 Å °-0.0049430478564 Å °0.0160601130126 Å °0.0463408623607 Å °-0.721874027854 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND ( RESID 1:105 OR RESID 201:209 OR RESID 210:210 ) ) OR ( CHAIN A AND ( RESID 201:202 OR RESID 1:105 OR RESID 203:203 ) ) OR ( CHAIN B AND ( RESID 201:207 OR RESID 208:208 OR RESID 1:105 ) ) OR ( CHAIN D AND ( RESID 201:207 OR RESID 1:105 OR RESID 208:208 ) )C1 - 105
2X-RAY DIFFRACTION1( CHAIN C AND ( RESID 1:105 OR RESID 201:209 OR RESID 210:210 ) ) OR ( CHAIN A AND ( RESID 201:202 OR RESID 1:105 OR RESID 203:203 ) ) OR ( CHAIN B AND ( RESID 201:207 OR RESID 208:208 OR RESID 1:105 ) ) OR ( CHAIN D AND ( RESID 201:207 OR RESID 1:105 OR RESID 208:208 ) )C201 - 209
3X-RAY DIFFRACTION1( CHAIN C AND ( RESID 1:105 OR RESID 201:209 OR RESID 210:210 ) ) OR ( CHAIN A AND ( RESID 201:202 OR RESID 1:105 OR RESID 203:203 ) ) OR ( CHAIN B AND ( RESID 201:207 OR RESID 208:208 OR RESID 1:105 ) ) OR ( CHAIN D AND ( RESID 201:207 OR RESID 1:105 OR RESID 208:208 ) )C210
4X-RAY DIFFRACTION1( CHAIN C AND ( RESID 1:105 OR RESID 201:209 OR RESID 210:210 ) ) OR ( CHAIN A AND ( RESID 201:202 OR RESID 1:105 OR RESID 203:203 ) ) OR ( CHAIN B AND ( RESID 201:207 OR RESID 208:208 OR RESID 1:105 ) ) OR ( CHAIN D AND ( RESID 201:207 OR RESID 1:105 OR RESID 208:208 ) )A201 - 202
5X-RAY DIFFRACTION1( CHAIN C AND ( RESID 1:105 OR RESID 201:209 OR RESID 210:210 ) ) OR ( CHAIN A AND ( RESID 201:202 OR RESID 1:105 OR RESID 203:203 ) ) OR ( CHAIN B AND ( RESID 201:207 OR RESID 208:208 OR RESID 1:105 ) ) OR ( CHAIN D AND ( RESID 201:207 OR RESID 1:105 OR RESID 208:208 ) )A1 - 105
6X-RAY DIFFRACTION1( CHAIN C AND ( RESID 1:105 OR RESID 201:209 OR RESID 210:210 ) ) OR ( CHAIN A AND ( RESID 201:202 OR RESID 1:105 OR RESID 203:203 ) ) OR ( CHAIN B AND ( RESID 201:207 OR RESID 208:208 OR RESID 1:105 ) ) OR ( CHAIN D AND ( RESID 201:207 OR RESID 1:105 OR RESID 208:208 ) )A203
7X-RAY DIFFRACTION1( CHAIN C AND ( RESID 1:105 OR RESID 201:209 OR RESID 210:210 ) ) OR ( CHAIN A AND ( RESID 201:202 OR RESID 1:105 OR RESID 203:203 ) ) OR ( CHAIN B AND ( RESID 201:207 OR RESID 208:208 OR RESID 1:105 ) ) OR ( CHAIN D AND ( RESID 201:207 OR RESID 1:105 OR RESID 208:208 ) )B201 - 207
8X-RAY DIFFRACTION1( CHAIN C AND ( RESID 1:105 OR RESID 201:209 OR RESID 210:210 ) ) OR ( CHAIN A AND ( RESID 201:202 OR RESID 1:105 OR RESID 203:203 ) ) OR ( CHAIN B AND ( RESID 201:207 OR RESID 208:208 OR RESID 1:105 ) ) OR ( CHAIN D AND ( RESID 201:207 OR RESID 1:105 OR RESID 208:208 ) )B208
9X-RAY DIFFRACTION1( CHAIN C AND ( RESID 1:105 OR RESID 201:209 OR RESID 210:210 ) ) OR ( CHAIN A AND ( RESID 201:202 OR RESID 1:105 OR RESID 203:203 ) ) OR ( CHAIN B AND ( RESID 201:207 OR RESID 208:208 OR RESID 1:105 ) ) OR ( CHAIN D AND ( RESID 201:207 OR RESID 1:105 OR RESID 208:208 ) )B1 - 105
10X-RAY DIFFRACTION1( CHAIN C AND ( RESID 1:105 OR RESID 201:209 OR RESID 210:210 ) ) OR ( CHAIN A AND ( RESID 201:202 OR RESID 1:105 OR RESID 203:203 ) ) OR ( CHAIN B AND ( RESID 201:207 OR RESID 208:208 OR RESID 1:105 ) ) OR ( CHAIN D AND ( RESID 201:207 OR RESID 1:105 OR RESID 208:208 ) )D201 - 207
11X-RAY DIFFRACTION1( CHAIN C AND ( RESID 1:105 OR RESID 201:209 OR RESID 210:210 ) ) OR ( CHAIN A AND ( RESID 201:202 OR RESID 1:105 OR RESID 203:203 ) ) OR ( CHAIN B AND ( RESID 201:207 OR RESID 208:208 OR RESID 1:105 ) ) OR ( CHAIN D AND ( RESID 201:207 OR RESID 1:105 OR RESID 208:208 ) )D1 - 105
12X-RAY DIFFRACTION1( CHAIN C AND ( RESID 1:105 OR RESID 201:209 OR RESID 210:210 ) ) OR ( CHAIN A AND ( RESID 201:202 OR RESID 1:105 OR RESID 203:203 ) ) OR ( CHAIN B AND ( RESID 201:207 OR RESID 208:208 OR RESID 1:105 ) ) OR ( CHAIN D AND ( RESID 201:207 OR RESID 1:105 OR RESID 208:208 ) )D208

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