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- PDB-9kfv: Crystal structure of the methyltransferase-ribozyme 1 bound to DN... -

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Basic information

Entry
Database: PDB / ID: 9kfv
TitleCrystal structure of the methyltransferase-ribozyme 1 bound to DNA substrate (1-benzyl-adenosine derivative)
Components
  • DNA (5'-D(*CP*CP*AP*CP*TP*GP*(A1EFN)P*GP*AP*GP*CP*TP*TP*C)-3')
  • RNA (5'-R(*GP*CP*UP*GP*GP*GP*AP*CP*AP*AP*CP*UP*AP*GP*AP*CP*AP*UP*AP*CP*AP*GP*UP*G)-3')
  • RNA (5'-R(*GP*GP*AP*AP*GP*CP*UP*CP*UP*GP*AP*CP*CP*GP*AP*CP*CP*CP*CP*CP*AP*GP*CP*C)-3')
KeywordsDNA-RNA HYBRID / Ribozyme / Methyltransferase / MTR1 / O6-benzylguanine
Function / homologyGUANINE / : / DNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsHe, Y. / Yan, K. / Lilley, D.M.J. / Huang, L.
Funding support China, United Kingdom, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171191 China
Engineering and Physical Sciences Research CouncilEP/X01567X/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of the methyltransferase ribozyme MTR1 bound to DNA substrate
Authors: He, Y. / Yan, K. / Lilley, D.M.J. / Huang, L.
History
DepositionNov 7, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 17, 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: DNA (5'-D(*CP*CP*AP*CP*TP*GP*(A1EFN)P*GP*AP*GP*CP*TP*TP*C)-3')
B: RNA (5'-R(*GP*GP*AP*AP*GP*CP*UP*CP*UP*GP*AP*CP*CP*GP*AP*CP*CP*CP*CP*CP*AP*GP*CP*C)-3')
C: RNA (5'-R(*GP*CP*UP*GP*GP*GP*AP*CP*AP*AP*CP*UP*AP*GP*AP*CP*AP*UP*AP*CP*AP*GP*UP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0048
Polymers19,7283
Non-polymers2755
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-19 kcal/mol
Surface area9780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.342, 67.342, 65.163
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

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DNA chain , 1 types, 1 molecules A

#1: DNA chain DNA (5'-D(*CP*CP*AP*CP*TP*GP*(A1EFN)P*GP*AP*GP*CP*TP*TP*C)-3')


Mass: 4330.889 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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RNA chain , 2 types, 2 molecules BC

#2: RNA chain RNA (5'-R(*GP*GP*AP*AP*GP*CP*UP*CP*UP*GP*AP*CP*CP*GP*AP*CP*CP*CP*CP*CP*AP*GP*CP*C)-3')


Mass: 7641.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-R(*GP*CP*UP*GP*GP*GP*AP*CP*AP*AP*CP*UP*AP*GP*AP*CP*AP*UP*AP*CP*AP*GP*UP*G)-3')


Mass: 7755.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 5 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5O
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K

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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: 3.79 Å3/Da / Density % sol: 67.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 100mM NaCl, 100mM LiCl, 10mM MgCl2, 36% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.82→67.34 Å / Num. obs: 6850 / % possible obs: 95.5 % / Redundancy: 6.1 % / CC1/2: 0.987 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.062 / Net I/σ(I): 10.5
Reflection shellResolution: 2.82→2.97 Å / Redundancy: 5 % / Rmerge(I) obs: 2.918 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1045 / CC1/2: 0.417 / Rpim(I) all: 1.443 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.82→33.67 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2339 284 4.61 %
Rwork0.1974 --
obs0.199 6160 86.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.82→33.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1307 15 0 1322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081473
X-RAY DIFFRACTIONf_angle_d1.3792282
X-RAY DIFFRACTIONf_dihedral_angle_d15.218700
X-RAY DIFFRACTIONf_chiral_restr0.055292
X-RAY DIFFRACTIONf_plane_restr0.00864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.82-3.550.3166970.2812712X-RAY DIFFRACTION79
3.55-33.670.21821870.17543164X-RAY DIFFRACTION93

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