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- PDB-8sv4: 7-Deazapurines and 5-Halogenpyrimidine DNA duplex -

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Basic information

Entry
Database: PDB / ID: 8sv4
Title7-Deazapurines and 5-Halogenpyrimidine DNA duplex
Components
  • DNA (5'-D(*(B86)P*(7DD)P*(B86)P*(7DD)P*(7DA)P*(7DA)P*(UCL)P*(UCL)P*(B86)P*(7DD)P*(B86)P*(7DD))-3')
  • Ribonuclease H
KeywordsDNA BINDING PROTEIN/DNA / 7-Deazapurines / 5-Halogenpyrimidines / Adenine-Tract Geometry / RNase-H complex / DNA duplex / Dickerson-Drew Dodecamer / DNA duplex crystal structure / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
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 / 2-[2-(2-ethoxyethoxy)ethoxy]ethanol / 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 Germany, 1items
OrganizationGrant numberCountry
Volkswagen Foundation92 851 Germany
CitationJournal: Biochemistry / Year: 2023
Title: Conformational Morphing by a DNA Analogue Featuring 7-Deazapurines and 5-Halogenpyrimidines and the Origins of Adenine-Tract Geometry.
Authors: Pallan, P.S. / Lybrand, T.P. / Rozners, E. / Abramov, M. / Schepers, G. / Eremeeva, E. / Herdewijn, P. / Egli, M.
History
DepositionMay 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease H
B: DNA (5'-D(*(B86)P*(7DD)P*(B86)P*(7DD)P*(7DA)P*(7DA)P*(UCL)P*(UCL)P*(B86)P*(7DD)P*(B86)P*(7DD))-3')
C: DNA (5'-D(*(B86)P*(7DD)P*(B86)P*(7DD)P*(7DA)P*(7DA)P*(UCL)P*(UCL)P*(B86)P*(7DD)P*(B86)P*(7DD))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2619
Polymers23,7103
Non-polymers5516
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.539, 92.539, 78.896
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

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Protein / DNA chain , 2 types, 3 molecules ABC

#1: Protein Ribonuclease H / RNase H


Mass: 16329.478 Da / Num. of mol.: 1 / 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(*(B86)P*(7DD)P*(B86)P*(7DD)P*(7DA)P*(7DA)P*(UCL)P*(UCL)P*(B86)P*(7DD)P*(B86)P*(7DD))-3')


Mass: 3690.286 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 85 molecules

#3: Chemical ChemComp-FWN / 2-[2-(2-ethoxyethoxy)ethoxy]ethanol


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 4.09 Å3/Da / Density % sol: 69.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2 M Ammonium Sulfate, 0.1 M Sodium acetate trihydrate and 25% (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: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 19, 2017
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.3→27.6 Å / Num. obs: 17002 / % possible obs: 98.9 % / Redundancy: 13.8 % / Rpim(I) all: 0.044 / Rrim(I) all: 0.166 / Χ2: 0.749 / Net I/σ(I): 4.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.3-2.387.11.47115730.5950.8640.4851.5570.52690.8
2.38-2.4810.11.32816610.780.9360.4041.3920.53898.3
2.48-2.5913.51.27717000.8420.9560.3551.3260.54599.9
2.59-2.7315.30.93817210.9180.9790.2480.970.581100
2.73-2.915.40.67717060.9450.9860.1790.7010.602100
2.9-3.1215.40.32317030.990.9980.0850.3350.663100
3.12-3.4315.40.15617360.9970.9990.0410.1610.825100
3.43-3.9315.40.11117000.9970.9990.0290.1151.064100
3.93-4.9515.30.07117380.99910.0190.0740.983100
4.95-27.614.80.05117640.99910.0140.0530.92100

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→27.6 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.037 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25355 870 5.1 %RANDOM
Rwork0.2139 ---
obs0.21599 16084 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.228 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20.63 Å20 Å2
2--1.27 Å2-0 Å2
3----4.11 Å2
Refinement stepCycle: 1 / Resolution: 2.3→27.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1076 494 34 79 1683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021685
X-RAY DIFFRACTIONr_bond_other_d0.0020.021279
X-RAY DIFFRACTIONr_angle_refined_deg1.5672.2682379
X-RAY DIFFRACTIONr_angle_other_deg0.82933018
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9755131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29125.19252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.29415204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.643155
X-RAY DIFFRACTIONr_chiral_restr0.4020.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021465
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02272
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_it3.324.453529
X-RAY DIFFRACTIONr_mcbond_other3.34.445526
X-RAY DIFFRACTIONr_mcangle_it4.8516.661657
X-RAY DIFFRACTIONr_mcangle_other4.8496.662658
X-RAY DIFFRACTIONr_scbond_it5.1595.3821156
X-RAY DIFFRACTIONr_scbond_other5.1595.3821156
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.6167.9321723
X-RAY DIFFRACTIONr_long_range_B_refined9.49251.8122089
X-RAY DIFFRACTIONr_long_range_B_other9.49451.812089
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å
RfactorNum. reflection% reflection
Rfree0.359 44 -
Rwork0.416 1050 -
obs--86.89 %

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