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- PDB-9mfh: env2 cobalamin riboswitch aptamer domain in the apo state -

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Basic information

Entry
Database: PDB / ID: 9mfh
Titleenv2 cobalamin riboswitch aptamer domain in the apo state
ComponentsRNA (76-MER)
KeywordsRNA / riboswitch / aptamer / vitamin B12 / cobalamin
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesmarine metagenome (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsOlenginski, L.T. / Batey, R.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM152029 United States
CitationJournal: Nat.Chem.Biol. / Year: 2025
Title: Designing small molecules targeting a cryptic RNA binding site through base displacement.
Authors: Olenginski, L.T. / Wierzba, A.J. / Laursen, S.P. / Batey, R.T.
History
DepositionDec 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7669
Polymers24,5721
Non-polymers1948
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.326, 39.320, 64.189
Angle α, β, γ (deg.)90.00, 121.18, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-291-

HOH

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Components

#1: RNA chain RNA (76-MER)


Mass: 24571.738 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) marine metagenome (others)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 303.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% (v/v) (+/-)-2-Methyl-2,4-pentanediol, 40 mM Sodium cacodylate trihydrate (pH 7.0), 12 mM Spermine tetrahydrochloride, 80 mM Potassium chloride, 20 mM Magnesium chloride hexahydrate. Hanging drop. 303.15 K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 7804 / % possible obs: 94.2 % / Redundancy: 2.4 % / CC1/2: 0.925 / Rpim(I) all: 0.083 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.5-2.591.80.2555810.8570.9610.2120.3341.04370.9
2.59-2.692.10.2617260.840.9560.2080.336188.3
2.69-2.812.30.2167850.8930.9710.1660.2740.98395.8
2.81-2.962.40.2027950.8970.9730.1560.2571.23998.1
2.96-3.152.50.1618020.9320.9820.1240.2041.57498.5
3.15-3.392.50.1258270.950.9870.0950.1581.81698.7
3.39-3.732.60.1118120.9480.9870.0830.1391.96399.1
3.73-4.262.50.18270.960.990.0760.1262.01299.2
4.26-5.352.50.0818280.9720.9930.0630.1032.10698.1
5.35-202.40.0618210.9960.9990.0480.078294.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→19.65 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.294 645 10.03 %
Rwork0.2422 --
obs0.2474 6433 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1631 8 181 1820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021828
X-RAY DIFFRACTIONf_angle_d0.6372848
X-RAY DIFFRACTIONf_dihedral_angle_d14.57909
X-RAY DIFFRACTIONf_chiral_restr0.033380
X-RAY DIFFRACTIONf_plane_restr0.00576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.910.42851240.33081132X-RAY DIFFRACTION97
2.91-3.20.35911360.2811154X-RAY DIFFRACTION99
3.2-3.660.27681250.21911161X-RAY DIFFRACTION99
3.66-4.60.24831280.22591168X-RAY DIFFRACTION99
4.6-19.650.26881320.22411173X-RAY DIFFRACTION96

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