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- PDB-8cu0: 12-mer DNA structure of ExBIM bound to RNaseH -modified DDD -

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Basic information

Entry
Database: PDB / ID: 8cu0
Title12-mer DNA structure of ExBIM bound to RNaseH -modified DDD
Components
  • DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*(OWR)P*CP*CP*G)-3')
  • Ribonuclease H
KeywordsDNA / alkylation / base stacking / DNA damage / H-bonding / 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 / Ribonuclease H domain / RNase H type-1 domain profile. / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Ribonuclease H
Similarity search - Component
Biological speciesHalalkalibacterium halodurans (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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*GP*GP*CP*AP*TP*GP*(OWR)P*CP*CP*G)-3')
E: DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*(OWR)P*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,11017
Polymers56,4315
Non-polymers67912
Water4,107228
1
C: Ribonuclease H
D: DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*(OWR)P*CP*CP*G)-3')
E: DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*(OWR)P*CP*CP*G)-3')
hetero molecules

A: Ribonuclease H
hetero molecules

B: Ribonuclease H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,11017
Polymers56,4315
Non-polymers67912
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Unit cell
Length a, b, c (Å)36.894, 89.403, 73.890
Angle α, β, γ (deg.)90.000, 101.420, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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.) Halalkalibacterium halodurans (bacteria)
Gene: rnhA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KEI9, ribonuclease H
#2: DNA chain DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*(OWR)P*CP*CP*G)-3')


Mass: 3721.473 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 240 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate trihydrate, 30% PEG 8000 (W/V)

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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
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.74→28.6 Å / Num. obs: 47425 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Biso Wilson estimate: 28.72 Å2 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.04 / Net I/σ(I): 22.11
Reflection shellResolution: 1.74→1.81 Å / Rmerge(I) obs: 1.585 / Mean I/σ(I) obs: 0.63 / Num. unique obs: 4470 / CC1/2: 0.327 / Rpim(I) all: 0.716 / Rrim(I) all: 1.749 / % possible all: 93.9

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Processing

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

3ey1


Resolution: 1.74→28.49 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2463 2801 5.98 %
Rwork0.2018 44049 -
obs0.2045 46850 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.96 Å2 / Biso mean: 32.6016 Å2 / Biso min: 17 Å2
Refinement stepCycle: final / Resolution: 1.74→28.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3212 496 42 228 3978
Biso mean--41.23 37.81 -
Num. residues----419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083874
X-RAY DIFFRACTIONf_angle_d1.0185338
X-RAY DIFFRACTIONf_dihedral_angle_d19.409666
X-RAY DIFFRACTIONf_chiral_restr0.061579
X-RAY DIFFRACTIONf_plane_restr0.007582
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.74-1.770.36391140.31441819193381
1.77-1.810.30691380.31142066220493
1.81-1.840.32861400.282174231497
1.84-1.880.29621370.26782173231098
1.88-1.920.30791340.26532205233998
1.92-1.960.32351540.25192211236599
1.96-2.010.28791330.23622223235699
2.01-2.070.25721430.21982238238199
2.07-2.130.2521250.21722219234499
2.13-2.20.29721410.21282249239099
2.2-2.280.26691390.212233237299
2.28-2.370.25181630.211822132376100
2.37-2.470.26521520.212622452397100
2.47-2.60.26791260.21342239236599
2.61-2.770.30661060.21822652371100
2.77-2.980.25951510.220722442395100
2.98-3.280.27351460.206922452391100
3.28-3.750.22381360.184222862422100
3.76-4.730.2041470.161122562403100
4.73-28.490.20391760.17592246242299

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