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- PDB-9e5h: env2 cobalamin riboswitch aptamer domain in complex with cyanocob... -

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Basic information

Entry
Database: PDB / ID: 9e5h
Titleenv2 cobalamin riboswitch aptamer domain in complex with cyanocobalamin
ComponentsRNA (76-MER)
KeywordsRNA / riboswitch / aptamer / vitamin B12 / cobalamin
Function / homologyCYANOCOBALAMIN / : / N-methylpropane-1,3-diamine / RNA / RNA (> 10)
Function and homology information
Biological speciesmarine metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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
DepositionOct 28, 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)
B: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,11228
Polymers49,4632
Non-polymers3,64926
Water4,576254
1
A: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,55614
Polymers24,7321
Non-polymers1,82513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,55614
Polymers24,7321
Non-polymers1,82513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.860, 114.486, 63.640
Angle α, β, γ (deg.)90.00, 99.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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RNA chain , 1 types, 2 molecules AB

#1: RNA chain RNA (76-MER)


Mass: 24731.697 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) marine metagenome (others)

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Non-polymers , 6 types, 280 molecules

#2: Chemical ChemComp-CNC / CYANOCOBALAMIN


Mass: 1356.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C63H89CoN14O14P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-N3D / N-methylpropane-1,3-diamine


Mass: 88.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12N2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.68 Å3/Da / Density % sol: 54.09 %
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: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0972 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0972 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 25277 / % possible obs: 95.3 % / Redundancy: 3.1 % / CC1/2: 0.973 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.067 / Rrim(I) all: 0.119 / Χ2: 1.01 / Net I/σ(I): 18.7 / Num. measured all: 3480275
Reflection shellResolution: 2.2→2.28 Å / % possible obs: 57.5 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 2.4 / Num. measured all: 30904 / Num. unique obs: 2131 / CC1/2: 0.88 / Rpim(I) all: 0.217 / Rrim(I) all: 0.389 / Χ2: 0.87 / Net I/σ(I) obs: 0.3 / % possible all: 80.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.66 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 34.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2783 995 7.92 %
Rwork0.2081 --
obs0.2138 12560 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3280 234 254 3768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073904
X-RAY DIFFRACTIONf_angle_d1.496104
X-RAY DIFFRACTIONf_dihedral_angle_d16.2411904
X-RAY DIFFRACTIONf_chiral_restr0.058766
X-RAY DIFFRACTIONf_plane_restr0.01156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.950.37361400.28351640X-RAY DIFFRACTION99
2.95-3.130.3221430.23791659X-RAY DIFFRACTION99
3.13-3.370.32471430.20761665X-RAY DIFFRACTION98
3.37-3.710.23921420.20271645X-RAY DIFFRACTION97
3.71-4.240.26111420.20791657X-RAY DIFFRACTION99
4.24-5.320.26611430.18451661X-RAY DIFFRACTION98
5.33-19.660.2511420.19651638X-RAY DIFFRACTION96

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