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- PDB-9e5r: env2 cobalamin riboswitch aptamer domain in complex with ethynyl-... -

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Basic information

Entry
Database: PDB / ID: 9e5r
Titleenv2 cobalamin riboswitch aptamer domain in complex with ethynyl-N-ethylpropiolamide-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: 2.34 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)52,84826
Polymers49,3032
Non-polymers3,54524
Water4,576254
1
A: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,42413
Polymers24,6521
Non-polymers1,77212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,42413
Polymers24,6521
Non-polymers1,77212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.878, 77.954, 80.006
Angle α, β, γ (deg.)90.00, 90.59, 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, 278 molecules

#2: Chemical ChemComp-A1BEZ / ethynyl-N-ethylpropiolamide-cobalamin / [(2~{R},3~{S},4~{R},5~{S})-5-(5,6-dimethylbenzimidazol-1-yl)-2-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] [(2~{R})-1-[3-[(3~{R},4~{R},5~{R},9~{S},14~{S},15~{S},19~{S},20~{S},21~{R},22~{R})-4,15,20-tris(2-azanyl-2-oxidanylidene-ethyl)-9,14,19-tris(3-azanyl-3-oxidanylidene-propyl)-1-[3-(ethylamino)-3-oxidanylidene-prop-1-ynyl]-5,7,10,10,15,17,20,21-octamethyl-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: 1426.463 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C67H95CoN14O15P / 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.: 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: 2.59 Å3/Da / Density % sol: 52.42 %
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: Mar 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.34→20 Å / Num. obs: 19966 / % possible obs: 94.3 % / Redundancy: 2.8 % / CC1/2: 0.99 / Rpim(I) all: 0.08 / Rrim(I) all: 0.143 / Χ2: 1.573 / Net I/av σ(I): 11.2 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.35-2.432.40.28815360.90.9730.2090.3580.71771.6
2.43-2.532.60.28117340.9150.9770.1950.3430.75484.3
2.53-2.652.70.26219930.9350.9830.1830.3210.81694.6
2.65-2.792.80.22320820.9510.9870.1530.2720.94398.6
2.79-2.962.90.1920910.9610.990.1320.2321.29599.1
2.96-3.192.90.14920810.9750.9940.10.1811.73298.9
3.19-3.512.90.12721010.9780.9940.0870.1552.03199.1
3.51-4.012.90.11520860.9760.9940.0780.142.17598.9
4.01-5.042.90.121140.9780.9940.0680.1212.24799
5.04-202.70.06821480.9890.9970.0490.0842.29198.9

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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: 2.34→19.77 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.276 1919 9.78 %
Rwork0.2065 --
obs0.2134 19630 92.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.34→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3272 228 254 3754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093892
X-RAY DIFFRACTIONf_angle_d1.6466084
X-RAY DIFFRACTIONf_dihedral_angle_d16.3041916
X-RAY DIFFRACTIONf_chiral_restr0.072786
X-RAY DIFFRACTIONf_plane_restr0.011170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.40.4527910.2843827X-RAY DIFFRACTION60
2.4-2.460.36271080.30481050X-RAY DIFFRACTION78
2.46-2.530.43421410.29181203X-RAY DIFFRACTION88
2.53-2.620.44281240.29991286X-RAY DIFFRACTION94
2.62-2.710.39351410.31371336X-RAY DIFFRACTION97
2.71-2.820.40631510.31991322X-RAY DIFFRACTION98
2.82-2.940.41741420.32061320X-RAY DIFFRACTION95
2.94-3.10.34341410.26141298X-RAY DIFFRACTION95
3.1-3.290.32171410.22121325X-RAY DIFFRACTION97
3.29-3.550.29961420.20291331X-RAY DIFFRACTION97
3.55-3.90.2651450.18591329X-RAY DIFFRACTION97
3.9-4.460.19721400.15881360X-RAY DIFFRACTION97
4.46-5.60.18811510.13191350X-RAY DIFFRACTION98
5.6-19.770.15981610.1411374X-RAY DIFFRACTION98

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