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- PDB-7mkt: Crystal structure of r(GU)11G-NMM complex -

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Basic information

Entry
Database: PDB / ID: 7mkt
TitleCrystal structure of r(GU)11G-NMM complex
ComponentsRNA (5'-R(*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*G)-3')
KeywordsRNA / RNA-porpyrin complex
Function / homology: / N-METHYLMESOPORPHYRIN / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 Å
AuthorsBingman, C.A. / Roschdi, S. / Nomura, Y. / Butcher, S.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2022
Title: An atypical RNA quadruplex marks RNAs as vectors for gene silencing.
Authors: Roschdi, S. / Yan, J. / Nomura, Y. / Escobar, C.A. / Petersen, R.J. / Bingman, C.A. / Tonelli, M. / Vivek, R. / Montemayor, E.J. / Wickens, M. / Kennedy, S.G. / Butcher, S.E.
History
DepositionApr 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2818
Polymers7,4651
Non-polymers8157
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.475, 42.483, 21.607
Angle α, β, γ (deg.)90.00, 90.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain RNA (5'-R(*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*G)-3')


Mass: 7465.337 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#2: Chemical ChemComp-MMP / N-METHYLMESOPORPHYRIN


Mass: 580.716 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H40N4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 52.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: The RNA smaple was prepared by mixing 1.44mM (GU)11G RNA and 1.44 mM NMM in 10 mM Tris, pH 7.03, and 100 mM KCl. An equal volume of RNA sample solution and reservoir solution were mixed and ...Details: The RNA smaple was prepared by mixing 1.44mM (GU)11G RNA and 1.44 mM NMM in 10 mM Tris, pH 7.03, and 100 mM KCl. An equal volume of RNA sample solution and reservoir solution were mixed and suspended over the reservoir solution consisting of 0.5 M Na/K tartarate, 0.1 M TrisHCl, pH 8.5, 5 mM NaOH. Cryoprotection: reservoir solution supplemented with 30% ethylene glycol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1271 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 27, 2020
RadiationMonochromator: Si <111> / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.239
11K, H, -L20.25
11-K, -H, -L30.242
11-h,-k,l40.269
ReflectionResolution: 1.97→21.61 Å / Num. obs: 5407 / % possible obs: 99.02 % / Redundancy: 6.7 % / Biso Wilson estimate: 63.54 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.05163 / Rpim(I) all: 0.0231 / Rrim(I) all: 0.05684 / Net I/σ(I): 16.09
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.7553 / Mean I/σ(I) obs: 1.57 / Num. unique obs: 529 / CC1/2: 0.966 / CC star: 0.991 / Rpim(I) all: 0.3083 / Rrim(I) all: 0.8172 / % possible all: 99.25

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.97→21.61 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.968 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Authors state that 4-way twin law was applied during refinement, while the validation program recalculated with different twin law. This causes the discrepancies between calculated and ...Details: Authors state that 4-way twin law was applied during refinement, while the validation program recalculated with different twin law. This causes the discrepancies between calculated and reported Rwork/Rfree values.
RfactorNum. reflection% reflectionSelection details
Rfree0.29145 476 8.8 %RANDOM
Rwork0.26869 ---
obs0.27053 4922 97.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 63.361 Å2
Baniso -1Baniso -2Baniso -3
1-20.86 Å20 Å29.54 Å2
2--9.07 Å20 Å2
3----29.93 Å2
Refinement stepCycle: 1 / Resolution: 1.97→21.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 493 49 0 542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.012597
X-RAY DIFFRACTIONr_bond_other_d0.0030.019258
X-RAY DIFFRACTIONr_angle_refined_deg1.0721.523928
X-RAY DIFFRACTIONr_angle_other_deg1.0962.214624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.721106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0560.292
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02338
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0286
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9526.716597
X-RAY DIFFRACTIONr_scbond_other2.9496.716596
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.18210.068929
X-RAY DIFFRACTIONr_long_range_B_refined6.78868.126901
X-RAY DIFFRACTIONr_long_range_B_other6.78468.125902
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.97→2.018 Å
RfactorNum. reflection% reflection
Rfree0.885 21 -
Rwork0.748 356 -
obs--93.09 %

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