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- PDB-8ctz: 12-mer DNA structure of ExBIM & O6Me-G bound to RNase-H -

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Basic information

Entry
Database: PDB / ID: 8ctz
Title12-mer DNA structure of ExBIM & O6Me-G bound to RNase-H
Components
  • DNA (5'-D(*CP*GP*CP*(6OG)P*AP*AP*TP*TP*(OWR)P*GP*CP*G)-3')
  • Ribonuclease H
KeywordsDNA / alkylation / base stacking / DNA damage / H-bonding / O6-methyl-2'-deoxyguanosine / ExBIM
Function / homology
Function and homology information


ribonuclease H / RNA-DNA hybrid ribonuclease activity / nucleic acid binding / metal ion binding / cytoplasm
Similarity search - Function
Ribonuclease H, Bacteroides-type / Ribonuclease H1, N-terminal / Ribonuclease H1, N-terminal domain superfamily / Caulimovirus viroplasmin / Ribosomal protein L9/RNase H1, N-terminal / RNase H type-1 domain profile. / Ribonuclease H domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
ACETATE ION / : / DNA / DNA (> 10) / Ribonuclease H
Similarity search - Component
Biological speciesAlkalihalobacillus halodurans (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsPallan, P.S. / Egli, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA160032 United States
CitationJournal: Chem.Res.Toxicol. / Year: 2022
Title: Conformation and Pairing Properties of an O 6 -Methyl-2'-deoxyguanosine-Directed Benzimidazole Nucleoside Analog in Duplex DNA.
Authors: Kellum Jr., A.H. / Pallan, P.S. / Nilforoushan, A. / Sturla, S.J. / Stone, M.P. / Egli, M.
History
DepositionMay 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease H
B: Ribonuclease H
C: Ribonuclease H
D: DNA (5'-D(*CP*GP*CP*(6OG)P*AP*AP*TP*TP*(OWR)P*GP*CP*G)-3')
E: DNA (5'-D(*CP*GP*CP*(6OG)P*AP*AP*TP*TP*(OWR)P*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,23117
Polymers56,4575
Non-polymers77412
Water2,144119
1
C: Ribonuclease H
hetero molecules

B: Ribonuclease H
D: DNA (5'-D(*CP*GP*CP*(6OG)P*AP*AP*TP*TP*(OWR)P*GP*CP*G)-3')
E: DNA (5'-D(*CP*GP*CP*(6OG)P*AP*AP*TP*TP*(OWR)P*GP*CP*G)-3')
hetero molecules

A: Ribonuclease H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,23117
Polymers56,4575
Non-polymers77412
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Unit cell
Length a, b, c (Å)59.506, 66.492, 69.182
Angle α, β, γ (deg.)90.000, 107.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / DNA chain , 2 types, 5 molecules ABCDE

#1: Protein Ribonuclease H / RNase H


Mass: 16329.478 Da / Num. of mol.: 3 / Mutation: D132N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alkalihalobacillus halodurans (bacteria)
Gene: rnhA / Plasmid: PET15B / Cell (production host): BL21 / Production host: Escherichia coli (E. coli) / Variant (production host): D132N / References: UniProt: Q9KEI9, ribonuclease H
#2: DNA chain DNA (5'-D(*CP*GP*CP*(6OG)P*AP*AP*TP*TP*(OWR)P*GP*CP*G)-3')


Mass: 3734.512 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 131 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 10% v/v 2-propanol and 20% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.32→29.75 Å / Num. obs: 22274 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 35.04 Å2 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.062 / Net I/σ(I): 14.63
Reflection shellResolution: 2.32→2.36 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1062 / CC1/2: 0.808 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EY1 (Protein alone)

3ey1


Resolution: 2.32→29.74 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2651 1091 4.92 %
Rwork0.1954 21070 -
obs0.1988 22161 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.6 Å2 / Biso mean: 38.042 Å2 / Biso min: 16.48 Å2
Refinement stepCycle: final / Resolution: 2.32→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3183 498 45 119 3845
Biso mean--46.32 45.04 -
Num. residues----416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083849
X-RAY DIFFRACTIONf_angle_d1.0435304
X-RAY DIFFRACTIONf_dihedral_angle_d19.946669
X-RAY DIFFRACTIONf_chiral_restr0.057574
X-RAY DIFFRACTIONf_plane_restr0.006579
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.32-2.420.38991400.25882412255292
2.42-2.550.32371240.24152649277399
2.55-2.710.2531390.21892636277599
2.71-2.920.34131320.219426392771100
2.92-3.210.28581450.19726392784100
3.21-3.680.25151440.180126822826100
3.68-4.630.23331200.158626932813100
4.63-29.740.23451470.20132720286799

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