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

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Basic information

Entry
Database: PDB / ID: 9elr
Titleenv2 cobalamin riboswitch aptamer domain in complex with ethynyl-2-naphthalenepropiolate-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: 2.2 Å
AuthorsOlenginski, L.T. / Wolters, T.A. / 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 4, 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)53,47529
Polymers49,4632
Non-polymers4,01227
Water7,494416
1
A: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,72514
Polymers24,7321
Non-polymers1,99413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,75015
Polymers24,7321
Non-polymers2,01814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.849, 78.181, 80.389
Angle α, β, γ (deg.)90.00, 90.36, 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, 443 molecules

#2: Chemical ChemComp-A1BI7 / naphthalen-2-yl 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-[3-[[(2~{R})-2-[[(2~{R},3~{S},4~{R},5~{S})-5-(5,6-dimethylbenzimidazol-1-yl)-2-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl]oxy-oxidanyl-phosphoryl]oxypropyl]amino]-3-oxidanylidene-propyl]-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-1-yl]prop-2-ynoate


Mass: 1525.549 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C75H96CoN13O16P / 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.: 19 / 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.: 416 / 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: 2.6 Å3/Da / Density % sol: 52.6 %
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: Oct 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 24041 / % possible obs: 93.3 % / Redundancy: 2.4 % / CC1/2: 0.99 / Rpim(I) all: 0.039 / Net I/σ(I): 18.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.2-2.282.10.12421320.9770.9940.1050.1630.66182.8
2.28-2.372.20.11122720.9810.9950.0920.1450.68289
2.37-2.482.30.11423880.9830.9960.0890.1450.78293.8
2.48-2.612.40.09924750.9860.9960.0760.1250.85696.1
2.61-2.772.50.08425130.990.9970.0630.1061.14597.5
2.77-2.982.50.06524710.9930.9980.0490.0821.61596.6
2.98-3.282.50.05524650.9940.9990.0410.0682.33596.2
3.28-3.762.50.04624770.9960.9990.0340.0572.59894.9
3.76-4.722.50.04624180.9940.9980.0340.0572.69493.6
4.72-202.40.04424300.9930.9980.0330.0552.72692.1

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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: 2.2→19.82 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2385 1963 8.24 %
Rwork0.1822 --
obs0.1869 23819 92.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3280 261 416 3957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083932
X-RAY DIFFRACTIONf_angle_d1.5116132
X-RAY DIFFRACTIONf_dihedral_angle_d15.0941940
X-RAY DIFFRACTIONf_chiral_restr0.067796
X-RAY DIFFRACTIONf_plane_restr0.012170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.28451160.21011311X-RAY DIFFRACTION77
2.25-2.310.34691280.23311439X-RAY DIFFRACTION86
2.31-2.380.32611340.22631549X-RAY DIFFRACTION90
2.38-2.460.35341320.24391550X-RAY DIFFRACTION93
2.46-2.540.35781400.24411629X-RAY DIFFRACTION95
2.54-2.650.34281540.25561591X-RAY DIFFRACTION96
2.65-2.770.36431530.2621637X-RAY DIFFRACTION96
2.77-2.910.31911420.23611599X-RAY DIFFRACTION94
2.91-3.090.27951430.21411592X-RAY DIFFRACTION95
3.09-3.330.20581460.18041614X-RAY DIFFRACTION95
3.33-3.660.20241410.16161601X-RAY DIFFRACTION94
3.66-4.190.20911460.13871579X-RAY DIFFRACTION93
4.19-5.260.16941400.13141574X-RAY DIFFRACTION92
5.26-19.820.16681480.1491591X-RAY DIFFRACTION91

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