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- PDB-8e2q: Crystal structure of TadAC-1.17 in a complex with ssDNA -

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Basic information

Entry
Database: PDB / ID: 8e2q
TitleCrystal structure of TadAC-1.17 in a complex with ssDNA
Components
  • DNA (5'-D(P*GP*CP*GP*GP*CP*TP*(D8A)P*CP*GP*GP*A)-3')
  • tRNA-specific adenosine deaminase 1.17
KeywordsDNA BINDING PROTEIN/DNA / deaminase / ssDNA / TadAC / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


tRNA(adenine34) deaminase / tRNA wobble adenosine to inosine editing / tRNA-specific adenosine-34 deaminase activity / zinc ion binding
Similarity search - Function
tRNA-specific adenosine deaminase / MafB19-like deaminase / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like
Similarity search - Domain/homology
DNA / DNA (> 10) / tRNA-specific adenosine deaminase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsFeliciano, P.R. / Lee, S.J. / Ciaramella, G.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat.Biotechnol. / Year: 2023
Title: Improved cytosine base editors generated from TadA variants.
Authors: Lam, D.K. / Feliciano, P.R. / Arif, A. / Bohnuud, T. / Fernandez, T.P. / Gehrke, J.M. / Grayson, P. / Lee, K.D. / Ortega, M.A. / Sawyer, C. / Schwaegerle, N.D. / Peraro, L. / Young, L. / ...Authors: Lam, D.K. / Feliciano, P.R. / Arif, A. / Bohnuud, T. / Fernandez, T.P. / Gehrke, J.M. / Grayson, P. / Lee, K.D. / Ortega, M.A. / Sawyer, C. / Schwaegerle, N.D. / Peraro, L. / Young, L. / Lee, S.J. / Ciaramella, G. / Gaudelli, N.M.
History
DepositionAug 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 31, 2023Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 25, 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: tRNA-specific adenosine deaminase 1.17
B: tRNA-specific adenosine deaminase 1.17
C: tRNA-specific adenosine deaminase 1.17
D: tRNA-specific adenosine deaminase 1.17
E: DNA (5'-D(P*GP*CP*GP*GP*CP*TP*(D8A)P*CP*GP*GP*A)-3')
F: DNA (5'-D(P*GP*CP*GP*GP*CP*TP*(D8A)P*CP*GP*GP*A)-3')
G: DNA (5'-D(P*GP*CP*GP*GP*CP*TP*(D8A)P*CP*GP*GP*A)-3')
H: DNA (5'-D(P*GP*CP*GP*GP*CP*TP*(D8A)P*CP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,58715
Polymers91,0498
Non-polymers5387
Water2,360131
1
A: tRNA-specific adenosine deaminase 1.17
B: tRNA-specific adenosine deaminase 1.17
E: DNA (5'-D(P*GP*CP*GP*GP*CP*TP*(D8A)P*CP*GP*GP*A)-3')
F: DNA (5'-D(P*GP*CP*GP*GP*CP*TP*(D8A)P*CP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7477
Polymers45,5254
Non-polymers2233
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-107 kcal/mol
Surface area15260 Å2
MethodPISA
2
C: tRNA-specific adenosine deaminase 1.17
D: tRNA-specific adenosine deaminase 1.17
G: DNA (5'-D(P*GP*CP*GP*GP*CP*TP*(D8A)P*CP*GP*GP*A)-3')
H: DNA (5'-D(P*GP*CP*GP*GP*CP*TP*(D8A)P*CP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8408
Polymers45,5254
Non-polymers3154
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-104 kcal/mol
Surface area14960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.930, 85.930, 224.590
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 6 through 12 or resid 14...
21(chain B and (resid 6 through 12 or resid 14...
31(chain C and (resid 6 through 12 or resid 14...
41(chain D and (resid 6 through 12 or resid 14...
12(chain E and resid 4 through 13)
22(chain G and resid 4 through 13)
32(chain H and resid 4 through 13)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PHEPHEMETMET(chain A and (resid 6 through 12 or resid 14...AA6 - 126 - 12
121HISHISILEILE(chain A and (resid 6 through 12 or resid 14...AA14 - 6014 - 60
131ALAALALEULEU(chain A and (resid 6 through 12 or resid 14...AA62 - 6362 - 63
141GLNGLNSERSER(chain A and (resid 6 through 12 or resid 14...AA65 - 9765 - 97
151ARGARGARGARG(chain A and (resid 6 through 12 or resid 14...AA9898
161VALVALASNASN(chain A and (resid 6 through 12 or resid 14...AA4 - 1574 - 157
171VALVALASNASN(chain A and (resid 6 through 12 or resid 14...AA4 - 1574 - 157
181VALVALASNASN(chain A and (resid 6 through 12 or resid 14...AA4 - 1574 - 157
191VALVALASNASN(chain A and (resid 6 through 12 or resid 14...AA4 - 1574 - 157
211PHEPHEMETMET(chain B and (resid 6 through 12 or resid 14...BB6 - 126 - 12
221HISHISLYSLYS(chain B and (resid 6 through 12 or resid 14...BB14 - 2014 - 20
231ARGARGALAALA(chain B and (resid 6 through 12 or resid 14...BB21 - 2221 - 22
241SERSERLYSLYS(chain B and (resid 6 through 12 or resid 14...BB2 - 1612 - 161
251SERSERLYSLYS(chain B and (resid 6 through 12 or resid 14...BB2 - 1612 - 161
261SERSERLYSLYS(chain B and (resid 6 through 12 or resid 14...BB2 - 1612 - 161
271SERSERLYSLYS(chain B and (resid 6 through 12 or resid 14...BB2 - 1612 - 161
311PHEPHEMETMET(chain C and (resid 6 through 12 or resid 14...CC6 - 126 - 12
321HISHISLYSLYS(chain C and (resid 6 through 12 or resid 14...CC14 - 2014 - 20
331ARGARGALAALA(chain C and (resid 6 through 12 or resid 14...CC21 - 2221 - 22
341VALVALGOLGOL(chain C and (resid 6 through 12 or resid 14...CC - L4 - 2014
351VALVALGOLGOL(chain C and (resid 6 through 12 or resid 14...CC - L4 - 2014
361VALVALGOLGOL(chain C and (resid 6 through 12 or resid 14...CC - L4 - 2014
371VALVALGOLGOL(chain C and (resid 6 through 12 or resid 14...CC - L4 - 2014
411PHEPHEMETMET(chain D and (resid 6 through 12 or resid 14...DD6 - 126 - 12
421HISHISLYSLYS(chain D and (resid 6 through 12 or resid 14...DD14 - 2014 - 20
431ARGARGALAALA(chain D and (resid 6 through 12 or resid 14...DD21 - 2221 - 22
441GLUGLUPHEPHE(chain D and (resid 6 through 12 or resid 14...DD3 - 1563 - 156
451GLUGLUPHEPHE(chain D and (resid 6 through 12 or resid 14...DD3 - 1563 - 156
461GLUGLUPHEPHE(chain D and (resid 6 through 12 or resid 14...DD3 - 1563 - 156
471GLUGLUPHEPHE(chain D and (resid 6 through 12 or resid 14...DD3 - 1563 - 156
112DCDCDADA(chain E and resid 4 through 13)EE4 - 134 - 13
212DCDCDADA(chain G and resid 4 through 13)GG4 - 134 - 13
312DCDCDADA(chain H and resid 4 through 13)HH4 - 134 - 13

NCS ensembles :
ID
1
2

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Components

#1: Protein
tRNA-specific adenosine deaminase 1.17


Mass: 18765.682 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tadA / Production host: Escherichia coli (E. coli) / References: UniProt: W8T8U5, tRNA(adenine34) deaminase
#2: DNA chain
DNA (5'-D(P*GP*CP*GP*GP*CP*TP*(D8A)P*CP*GP*GP*A)-3')


Mass: 3996.587 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3,350, tacsimate pH 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.28
ReflectionResolution: 2.34→62.03 Å / Num. obs: 41554 / % possible obs: 100 % / Redundancy: 9.1 % / CC1/2: 0.991 / Net I/σ(I): 7.7
Reflection shellResolution: 2.34→2.4 Å / Num. unique obs: 3041 / CC1/2: 0.47

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8E2P

8e2p


Resolution: 2.34→62.03 Å / Cross valid method: THROUGHOUT / σ(F): 224.59 / Phase error: 31.41 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2049 2085 5.02 %
Rwork0.169 39410 -
obs0.1802 41494 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.43 Å2 / Biso mean: 43.1387 Å2 / Biso min: 18.87 Å2
Refinement stepCycle: final / Resolution: 2.34→62.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4817 970 22 131 5940
Biso mean--46.71 44.45 -
Num. residues----668
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1696X-RAY DIFFRACTION6.947TORSIONAL
12B1696X-RAY DIFFRACTION6.947TORSIONAL
13C1696X-RAY DIFFRACTION6.947TORSIONAL
14D1696X-RAY DIFFRACTION6.947TORSIONAL
21E276X-RAY DIFFRACTION6.947TORSIONAL
22G276X-RAY DIFFRACTION6.947TORSIONAL
23H276X-RAY DIFFRACTION6.947TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.34-2.390.32361680.27642560272894
2.39-2.450.32971220.27712609273196
2.45-2.520.28831350.2782589272495
2.52-2.590.32951660.27042534270094
2.6-2.680.28311400.26382597273795
2.68-2.770.29081170.25972620273796
2.77-2.890.30241380.23712578271695
2.89-3.020.28441210.22352610273195
3.02-3.180.23871690.20782606277594
3.18-3.370.21841290.19232600272995
3.37-3.640.2261360.17282640277695
3.64-40.17981220.15212644276696
4-4.580.17881240.13492687281196
4.58-5.770.19371030.13132745284896
5.77-62.030.15451940.14342791298593

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