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- PDB-8sv3: 7-Deazapurines and 5-Halogenpyrimidine DNA duplex -

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Basic information

Entry
Database: PDB / ID: 8sv3
Title7-Deazapurines and 5-Halogenpyrimidine DNA duplex
Components
  • Modified DNA
  • 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


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
DNA / DNA (> 10) / Ribonuclease H
Similarity search - Component
Biological speciesHalalkalibacterium halodurans (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 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: Ribonuclease H
C: Ribonuclease H
D: Modified DNA
E: Modified DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5319
Polymers56,3695
Non-polymers1624
Water8,863492
1
A: Ribonuclease H
D: Modified DNA
E: Modified DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8265
Polymers23,7103
Non-polymers1162
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3522
Polymers16,3291
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ribonuclease H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3522
Polymers16,3291
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.983, 89.000, 72.566
Angle α, β, γ (deg.)90.00, 100.44, 90.00
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.) Halalkalibacterium halodurans (bacteria)
Gene: rnhA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KEI9, ribonuclease H
#2: DNA chain Modified DNA


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

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Non-polymers , 4 types, 496 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 2.08 Å3/Da / Density % sol: 40.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 2 M Ammonium Sulphate

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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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 8, 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: 1.51→50 Å / Num. obs: 72096 / % possible obs: 100 % / Redundancy: 4.5 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.028 / Rrim(I) all: 0.06 / Χ2: 1.37 / Net I/σ(I): 12.3 / Num. measured all: 327633
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.51-1.563.90.3771450.8570.9610.2140.4290.6999.8
1.56-1.634.50.28971740.920.9790.1540.3290.766100
1.63-1.74.60.21372050.9560.9890.1120.2420.82100
1.7-1.794.60.15371940.9780.9940.080.1730.925100
1.79-1.94.60.11671900.9860.9970.060.1311.097100
1.9-2.054.60.0972370.990.9980.0470.1021.487100
2.05-2.264.70.06971580.9930.9980.0360.0781.801100
2.26-2.584.70.05772380.9950.9990.0290.0641.811100
2.58-3.254.60.04872370.9960.9990.0260.0552.239100
3.25-504.60.03773180.9970.9990.020.0421.86599.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→44.54 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.477 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20968 3475 4.8 %RANDOM
Rwork0.17701 ---
obs0.17858 68594 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.124 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20.25 Å2
2---0.36 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.51→44.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3228 494 9 492 4223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0143978
X-RAY DIFFRACTIONr_bond_other_d00.0183417
X-RAY DIFFRACTIONr_angle_refined_deg1.9011.8625519
X-RAY DIFFRACTIONr_angle_other_deg1.3631.7067960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3565393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69523.787169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.84615608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5241515
X-RAY DIFFRACTIONr_chiral_restr0.4710.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.023971
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02786
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_it1.8051.8471582
X-RAY DIFFRACTIONr_mcbond_other1.7971.8451581
X-RAY DIFFRACTIONr_mcangle_it2.5722.7671973
X-RAY DIFFRACTIONr_mcangle_other2.5742.7691974
X-RAY DIFFRACTIONr_scbond_it2.8492.0952396
X-RAY DIFFRACTIONr_scbond_other2.8492.0962397
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2393.0323547
X-RAY DIFFRACTIONr_long_range_B_refined5.49421.6334863
X-RAY DIFFRACTIONr_long_range_B_other5.49421.6314863
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.51→1.549 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 237 -
Rwork0.236 4840 -
obs--94.97 %

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