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- PDB-9e5p: env2 cobalamin riboswitch aptamer domain in complex with ethynyl-... -

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Basic information

Entry
Database: PDB / ID: 9e5p
Titleenv2 cobalamin riboswitch aptamer domain in complex with ethynyl-benzofuran-cobalamin
ComponentsRNA (76-MER)
KeywordsRNA / riboswitch / aptamer / vitamin B12 / cobalamin
Function / homology: / : / N-methylpropane-1,3-diamine / RNA / RNA (> 10)
Function and homology information
Biological speciesmarine metagenome (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.36 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)52,97026
Polymers49,3032
Non-polymers3,66724
Water5,206289
1
A: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,48513
Polymers24,6521
Non-polymers1,83312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,48513
Polymers24,6521
Non-polymers1,83312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.112, 78.063, 80.115
Angle α, β, γ (deg.)90.00, 90.07, 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: 24651.719 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) marine metagenome (others)

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Non-polymers , 5 types, 313 molecules

#2: Chemical ChemComp-A1BEX / ethynyl-benzofuran-cobalamin / [(2~{R},3~{S},4~{R},5~{S})-5-(5,6-dimethylbenzimidazol-1-yl)-2-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] 1-[3-[(3~{R},4~{R},5~{R},9~{S},14~{S},15~{S},19~{S},20~{S},21~{R})-4,15,20-tris(2-azanyl-2-oxidanylidene-ethyl)-9,14,19-tris(3-azanyl-3-oxidanylidene-propyl)-5,7,10,10,15,17,20,21-octamethyl-1-[2-(1-oxidanylidene-3~{H}-2-benzofuran-5-yl)ethynyl]-22-aza-2,23,24-triazonia-1$l^{5}-cobaltaoctacyclo[11.9.1.1^{1,8}.0^{2,6}.0^{3,21}.0^{16,23}.0^{18,22}.0^{11,24}]tetracosa-2(6),7,11(24),12,16(23),17-hexaen-5-yl]propanoylamino]propan-2-yl hydrogen phosphate


Mass: 1487.501 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C72H94CoN13O16P / 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-MG / MAGNESIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.61 Å3/Da / Density % sol: 52.83 %
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: Feb 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.35→20 Å / Num. obs: 19366 / % possible obs: 92.6 % / Redundancy: 2.4 % / CC1/2: 0.99 / CC star: 0.99 / Rpim(I) all: 0.042 / Rrim(I) all: 0.073 / Χ2: 1.279 / Net I/σ(I): 12.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.35-2.431.90.24115830.9370.9840.1960.3120.62575.4
2.43-2.532.10.22617660.9410.9850.1760.2890.6385.4
2.53-2.652.20.19118830.9640.9910.1490.2440.6391.1
2.65-2.792.30.14219640.9810.9950.1090.180.84994.7
2.79-2.962.30.11519970.9870.9970.0860.1441.195.1
2.96-3.192.50.0819830.9920.9980.0590.11.41295.3
3.19-3.512.60.06119880.9950.9990.0430.0751.72395.6
3.51-4.012.70.05220270.9950.9990.0370.0641.71696.8
4.01-5.042.80.04720610.9960.9990.0320.0571.55297.7
5.04-202.70.03621140.9970.9990.0260.0441.53898.4

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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: 2.36→20 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2795 1899 9.91 %
Rwork0.1985 --
obs0.2065 19168 91.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.36→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3272 238 289 3799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093906
X-RAY DIFFRACTIONf_angle_d1.7116108
X-RAY DIFFRACTIONf_dihedral_angle_d16.681916
X-RAY DIFFRACTIONf_chiral_restr0.074786
X-RAY DIFFRACTIONf_plane_restr0.011170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.410.35281060.2473939X-RAY DIFFRACTION68
2.41-2.480.40571150.27931070X-RAY DIFFRACTION80
2.48-2.550.44031170.28661179X-RAY DIFFRACTION86
2.55-2.630.4151290.32111196X-RAY DIFFRACTION91
2.63-2.730.43541440.28871298X-RAY DIFFRACTION93
2.73-2.840.39081430.28831232X-RAY DIFFRACTION94
2.84-2.970.40231430.28461262X-RAY DIFFRACTION93
2.97-3.120.36171420.24221233X-RAY DIFFRACTION92
3.12-3.320.29561350.19961269X-RAY DIFFRACTION95
3.32-3.570.27671470.18531275X-RAY DIFFRACTION95
3.57-3.930.26371420.18331308X-RAY DIFFRACTION96
3.93-4.490.2311490.16431310X-RAY DIFFRACTION96
4.49-5.640.18661400.13731328X-RAY DIFFRACTION97
5.64-200.16211470.13951370X-RAY DIFFRACTION98

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