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- PDB-8e5e: Crystal structure of double-stranded DNA deaminase toxin DddA in ... -

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Basic information

Entry
Database: PDB / ID: 8e5e
TitleCrystal structure of double-stranded DNA deaminase toxin DddA in complex with DNA with the target cytosine flipped into the active site
Components
  • DNA (5'-D(*GP*CP*AP*AP*CP*GP*TP*CP*CP*GP*GP*TP*AP*C)-3')
  • DNA (5'-D(*GP*TP*AP*CP*CP*GP*GP*AP*CP*GP*TP*TP*GP*C)-3')
  • Double-stranded DNA deaminase toxin A
KeywordsTOXIN/DNA / toxin / DNA binding / deaminase / TOXIN-DNA complex
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines / toxin activity / hydrolase activity / membrane / metal ion binding
Similarity search - Function
Double-stranded DNA deaminase toxin A / Double-stranded DNA deaminase toxin A / Domain of unknown function DUF6531 / Domain of unknown function (DUF6531) / RHS protein / RHS protein / RHS repeat / RHS Repeat / PAAR motif / PAAR motif ...Double-stranded DNA deaminase toxin A / Double-stranded DNA deaminase toxin A / Domain of unknown function DUF6531 / Domain of unknown function (DUF6531) / RHS protein / RHS protein / RHS repeat / RHS Repeat / PAAR motif / PAAR motif / YD repeat / Rhs repeat-associated core
Similarity search - Domain/homology
DNA / DNA (> 10) / Double-stranded DNA deaminase toxin A
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsYin, L.L. / Shi, K. / Aihara, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01-CA234228 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2023
Title: Structural basis of sequence-specific cytosine deamination by double-stranded DNA deaminase toxin DddA.
Authors: Yin, L. / Shi, K. / Aihara, H.
History
DepositionAug 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Double-stranded DNA deaminase toxin A
C: DNA (5'-D(*GP*TP*AP*CP*CP*GP*GP*AP*CP*GP*TP*TP*GP*C)-3')
B: DNA (5'-D(*GP*CP*AP*AP*CP*GP*TP*CP*CP*GP*GP*TP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3385
Polymers23,2493
Non-polymers902
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-51 kcal/mol
Surface area10540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.950, 62.950, 237.078
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Double-stranded DNA deaminase toxin A / DddA / Cytidine deaminase / CD


Mass: 14686.213 Da / Num. of mol.: 1 / Mutation: E1347A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Gene: dddA / Production host: Escherichia coli (E. coli)
References: UniProt: P0DUH5, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines

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DNA chain , 2 types, 2 molecules CB

#2: DNA chain DNA (5'-D(*GP*TP*AP*CP*CP*GP*GP*AP*CP*GP*TP*TP*GP*C)-3')


Mass: 4296.791 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*AP*AP*CP*GP*TP*CP*CP*GP*GP*TP*AP*C)-3')


Mass: 4265.780 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 4 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 8.5, 25 % polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.62→44.87 Å / Num. obs: 8887 / % possible obs: 98 % / Redundancy: 5.7 % / CC1/2: 0.979 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.079 / Rrim(I) all: 0.171 / Χ2: 2.41 / Net I/σ(I): 45.6 / Num. measured all: 50693
Reflection shellResolution: 2.62→2.74 Å / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 1.762 / Num. measured all: 7585 / Num. unique obs: 1076 / CC1/2: 0.589 / Rpim(I) all: 0.706 / Rrim(I) all: 1.904 / Χ2: 1.18 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6U08

6u08


Resolution: 2.62→35.78 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.258 459 5.19 %
Rwork0.242 --
obs0.2428 8851 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.62→35.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms984 568 2 2 1556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d23.112633
X-RAY DIFFRACTIONf_chiral_restr0.035256
X-RAY DIFFRACTIONf_plane_restr0.003216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.710.3993460.4113814X-RAY DIFFRACTION100
2.71-2.820.466440.3829828X-RAY DIFFRACTION100
2.82-2.950.4409520.3676823X-RAY DIFFRACTION100
2.95-3.10.3601380.3785845X-RAY DIFFRACTION100
3.11-3.30.3071380.3093857X-RAY DIFFRACTION100
3.3-3.550.3335490.26838X-RAY DIFFRACTION100
3.55-3.910.264500.2616841X-RAY DIFFRACTION98
3.91-4.480.2025550.2154829X-RAY DIFFRACTION97
4.48-5.640.2258400.2007852X-RAY DIFFRACTION95
5.64-35.780.2171470.1932865X-RAY DIFFRACTION88
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6898-1.83750.01433.97082.74263.86180.229-0.0011-1.511-1.1019-1.4371.272-0.1562-0.92910.31810.5383-0.01930.11720.9844-0.07181.104-20.56651.5178-5.2966
26.29722.1309-0.17082.3823-1.89392.82280.4924-0.7816-0.22812.1173-0.2838-0.7256-0.92030.26260.46471.097-0.0833-0.05350.8901-0.09460.7413-21.846415.23918.4337
33.63361.0778-0.18958.6979-2.72595.86150.0673-0.5674-0.27120.1222-0.8228-1.2972-0.64250.91570.57260.5539-0.104-0.13030.88970.05160.9232-14.897517.1158-4.8875
47.4969-1.71454.91690.6641-0.5514.42230.0774-0.8483-0.66990.46830.54420.8466-1.1469-1.5364-0.15480.76090.16790.19970.9341-0.37090.9765-31.92620.8386-0.1335
57.16681.5379-2.25677.0093-1.46371.8313-0.2190.7291-0.0023-1.0046-0.11771.1358-0.9378-2.0608-0.03340.91920.0701-0.26591.0648-0.09330.9534-26.438317.1377-8.7396
65.80960.2818-0.50877.6612-2.6618.1584-0.98291.15970.656-1.64210.9882-1.6091-0.32731.41840.52451.1073-0.0209-0.06251.34320.17171.3402-9.693127.5832-14.7895
77.1714-0.0828-1.2044.42554.66165.03890.3399-0.9421.2602-0.5348-0.480.9787-1.8338-0.8773-0.05941.66810.0587-0.36611.1231-0.17431.3866-24.478237.0125-6.0945
86.15534.84613.11268.81745.79313.8669-0.05730.56450.9769-0.5012-0.59630.4617-2.50410.52270.0841.49220.1073-0.30711.0331-0.36571.1473-21.988338.255-3.2658
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1290 through 1299 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1300 through 1311 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1312 through 1393 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1394 through 1403 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1404 through 1413 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1414 through 1423 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 14 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 14 )

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