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- PDB-8cty: 12-mer DNA structure of ExBIM bound to RNase-H -

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Basic information

Entry
Database: PDB / ID: 8cty
Title12-mer DNA structure of ExBIM bound to RNase-H
Components
  • DNA (5'-D(*CP*GP*CP*GP*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


DNA replication, removal of RNA primer / 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 / Ribonuclease H1 N-terminal domain / : / 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 / DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / Ribonuclease H
Similarity search - Component
Biological speciesHalalkalibacterium halodurans (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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: Ribonuclease H
E: Ribonuclease H
F: Ribonuclease H
G: Ribonuclease H
H: Ribonuclease H
I: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OWR)P*GP*CP*G)-3')
J: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OWR)P*GP*CP*G)-3')
K: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OWR)P*GP*CP*G)-3')
L: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OWR)P*GP*CP*G)-3')
M: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OWR)P*GP*CP*G)-3')
N: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OWR)P*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,50436
Polymers152,95914
Non-polymers1,54522
Water4,774265
1
F: Ribonuclease H
M: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OWR)P*GP*CP*G)-3')
N: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OWR)P*GP*CP*G)-3')
hetero molecules

A: Ribonuclease H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,45710
Polymers40,1004
Non-polymers3576
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
2
B: Ribonuclease H
C: Ribonuclease H
G: Ribonuclease H
I: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OWR)P*GP*CP*G)-3')
J: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OWR)P*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,21716
Polymers56,4295
Non-polymers78711
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Ribonuclease H
K: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OWR)P*GP*CP*G)-3')
L: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OWR)P*GP*CP*G)-3')
hetero molecules

D: Ribonuclease H

H: Ribonuclease H


Theoretical massNumber of molelcules
Total (without water)56,83010
Polymers56,4295
Non-polymers4005
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_665x+1,y+1,z1
crystal symmetry operation1_655x+1,y,z1
Unit cell
Length a, b, c (Å)64.976, 65.834, 95.723
Angle α, β, γ (deg.)84.540, 88.200, 62.490
Int Tables number1
Space group name H-MP1

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Components

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Protein / DNA chain , 2 types, 14 molecules ABCDEFGHIJKLMN

#1: Protein
Ribonuclease H / RNase H


Mass: 16329.478 Da / Num. of mol.: 8 / 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*CP*GP*AP*AP*TP*TP*(OWR)P*GP*CP*G)-3')


Mass: 3720.485 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 7 types, 287 molecules

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


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES sodium pH = 7.5, 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: Apr 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.3→32.73 Å / Num. obs: 61160 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 38.07 Å2 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.053 / Net I/σ(I): 3.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.1 % / Rmerge(I) obs: 1.043 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 5899 / CC1/2: 0.386 / Rpim(I) all: 0.683 / % possible all: 94.4

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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

3ey1


Resolution: 2.3→32.73 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 26.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2606 3113 5.13 %
Rwork0.1958 57531 -
obs0.1989 60644 97.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.14 Å2 / Biso mean: 42.7127 Å2 / Biso min: 18.65 Å2
Refinement stepCycle: final / Resolution: 2.3→32.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8517 1382 99 265 10263
Biso mean--47.01 42.22 -
Num. residues----1113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910342
X-RAY DIFFRACTIONf_angle_d1.00214261
X-RAY DIFFRACTIONf_dihedral_angle_d21.2271790
X-RAY DIFFRACTIONf_chiral_restr0.0591550
X-RAY DIFFRACTIONf_plane_restr0.0071549
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.330.34631380.29522351248986
2.33-2.370.33621440.28212512265694
2.37-2.410.34191500.26562578272895
2.41-2.460.30861590.26612552271196
2.46-2.50.32511560.25482607276397
2.5-2.550.28721380.25162585272397
2.55-2.610.29161650.24392633279897
2.61-2.670.31951520.23682576272897
2.67-2.740.32321810.2322564274597
2.74-2.810.31811780.24072595277397
2.81-2.890.30161860.23042570275698
2.89-2.990.34331500.22452660281098
2.99-3.090.30941150.21212694280998
3.09-3.220.32271040.19942655275998
3.22-3.360.26551310.19172655278699
3.36-3.540.25541140.18882692280699
3.54-3.760.23421130.17082687280099
3.76-4.050.2036940.16292725281999
4.05-4.460.2391480.15722634278299
4.46-5.10.1729900.15382731282199
5.1-6.420.22361590.1842647280699
6.42-32.730.18781480.17422628277698

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