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- PDB-8e5d: Crystal structure of double-stranded DNA deaminase toxin DddA in ... -

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Basic information

Entry
Database: PDB / ID: 8e5d
TitleCrystal structure of double-stranded DNA deaminase toxin DddA in complex with DNA with the target cytosine parked in the major groove
Components
  • (DNA (5'-D(*GP*TP*AP*CP*CP*GP*GP*AP*CP*GP*TP*TP*GP*C)- ...) x 2
  • 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
PHOSPHATE ION / 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: 2.39 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*TP*AP*CP*CP*GP*GP*AP*CP*GP*TP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4336
Polymers23,2493
Non-polymers1853
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-62 kcal/mol
Surface area10830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.699, 94.611, 138.465
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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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 (5'-D(*GP*TP*AP*CP*CP*GP*GP*AP*CP*GP*TP*TP*GP*C)- ... , 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*TP*AP*CP*CP*GP*GP*AP*CP*GP*TP*TP*GP*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 , 4 types, 15 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: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 4.49 Å3/Da / Density % sol: 72.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium dihydrogen phosphate, 20 % 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 S 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: 2.39→47.15 Å / Num. obs: 13177 / % possible obs: 93.2 % / Redundancy: 5.1 % / Biso Wilson estimate: 47.22 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.042 / Rrim(I) all: 0.101 / Net I/av σ(I): 8.7 / Net I/σ(I): 5.1
Reflection shellResolution: 2.39→2.55 Å / Rmerge(I) obs: 1.139 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 659 / CC1/2: 0.804 / Rpim(I) all: 0.485 / Rrim(I) all: 1.24 / Rsym value: 1.139

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6U08

6u08


Resolution: 2.39→44.77 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2326 677 5.14 %
Rwork0.1979 --
obs0.1997 13172 76.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.39→44.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1004 568 7 12 1591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d25.812639
X-RAY DIFFRACTIONf_chiral_restr0.047258
X-RAY DIFFRACTIONf_plane_restr0.005220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.480.4224210.3942325X-RAY DIFFRACTION21
2.48-2.580.3711280.305471X-RAY DIFFRACTION30
2.58-2.70.3373460.2996690X-RAY DIFFRACTION43
2.7-2.840.292620.29261208X-RAY DIFFRACTION75
2.84-3.020.3154920.29121544X-RAY DIFFRACTION97
3.02-3.250.2641840.24831633X-RAY DIFFRACTION100
3.25-3.580.2764820.2131633X-RAY DIFFRACTION100
3.58-4.090.2265940.18561605X-RAY DIFFRACTION98
4.09-5.150.1673840.14451651X-RAY DIFFRACTION99
5.16-44.770.1788840.15611735X-RAY DIFFRACTION96
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)
11.12431.67020.47172.57581.14812.3064-0.4291-0.17720.5827-0.29920.15680.3001-0.3552-0.18170.3260.2412-0.0624-0.12590.5058-0.3150.50632.28520.1992-5.1203
20.6845-0.0326-0.66510.0645-0.23851.8001-0.2594-0.3541-0.01780.42170.00420.05470.39820.045-0.15720.6220.26290.09360.6967-0.14450.26544.4475-17.77663.1458
34.65440.7263-0.02972.07841.94283.2947-0.3612-0.36780.69680.1244-0.16820.60950.0018-0.16330.00730.17070.04980.0410.5111-0.23920.4601-6.9269-7.4808-3.1965
43.37690.242-0.10631.73950.95721.6767-0.2414-0.24150.30690.14190.0270.22420.08390.09720.20220.12910.06730.09160.3988-0.13890.3912-5.7407-17.3382-10.4999
55.089-0.7812-1.51936.40253.98426.0979-0.3251-0.14730.16170.17680.23670.2060.28940.4538-0.01110.1796-0.00560.06220.3833-0.10630.33254.2394-19.7125-12.6242
65.29744.18124.28363.81273.51175.8586-0.3317-0.38931.1615-0.3882-0.31050.6426-0.6501-0.45360.95080.16980.0747-0.05960.2688-0.18660.3447-2.0792-9.4064-15.8804
77.188-2.0723-1.23242.0919-0.88821.2462-0.2962-0.57030.20440.52520.4831-0.04680.210.5411-0.03980.15790.09720.00220.439-0.10170.204913.8742-18.9514-7.711
85.991-4.69654.82646.0303-2.71975.597-0.32760.18320.9413-0.30790.0614-0.88250.21160.22020.24020.1895-0.02220.03690.4743-0.07140.35157.8426-12.768-13.9532
98.23755.156-3.77947.0419-4.7177.2551-0.31-0.312-0.4165-1.1105-0.70240.4360.60550.45840.85170.20.0435-0.03240.3875-0.15690.3618-9.6683-25.2553-21.4943
104.80640.9641-0.38892.74961.87511.51910.0008-0.6074-0.90860.7928-0.2158-0.13180.80740.38010.2270.47610.06620.05990.50110.00950.36966.2836-32.8443-17.9004
115.2691-0.0394-1.2311.576-0.5523.675-0.1362-0.4288-0.80190.4940.42090.50141.3817-0.50070.82350.8795-0.04240.28250.60420.11970.44394.1946-35.4224-15.3617
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1290 through 1300 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1301 through 1311 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1312 through 1330 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1331 through 1366 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1367 through 1383 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1384 through 1393 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1394 through 1403 )
8X-RAY DIFFRACTION8chain 'A' and (resid 1404 through 1413 )
9X-RAY DIFFRACTION9chain 'A' and (resid 1414 through 1425 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 14 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 14 )

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