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- PDB-8e2r: Crystal structure of TadAC-1.14 -

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Basic information

Entry
Database: PDB / ID: 8e2r
TitleCrystal structure of TadAC-1.14
ComponentstRNA-specific adenosine deaminase 1.14
KeywordsDNA BINDING PROTEIN / deaminase / TadAC
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
MafB19-like deaminase / tRNA-specific adenosine 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
tRNA-specific adenosine deaminase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 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 1.14
B: tRNA-specific adenosine deaminase 1.14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8955
Polymers37,6722
Non-polymers2233
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-101 kcal/mol
Surface area12720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.740, 89.740, 112.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 6 through 25 or (resid 26...
21(chain B and (resid 6 through 12 or (resid 13...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEGLUGLU(chain A and (resid 6 through 25 or (resid 26...AA6 - 256 - 25
12ARGARGARGARG(chain A and (resid 6 through 25 or (resid 26...AA2626
13PHEPHEARGARG(chain A and (resid 6 through 25 or (resid 26...AA6 - 1506 - 150
14PHEPHEARGARG(chain A and (resid 6 through 25 or (resid 26...AA6 - 1506 - 150
15PHEPHEARGARG(chain A and (resid 6 through 25 or (resid 26...AA6 - 1506 - 150
16PHEPHEARGARG(chain A and (resid 6 through 25 or (resid 26...AA6 - 1506 - 150
21PHEPHEMETMET(chain B and (resid 6 through 12 or (resid 13...BB6 - 126 - 12
22ARGARGARGARG(chain B and (resid 6 through 12 or (resid 13...BB1313
23GLUGLUGOLGOL(chain B and (resid 6 through 12 or (resid 13...BB - D3 - 2013
24GLUGLUGOLGOL(chain B and (resid 6 through 12 or (resid 13...BB - D3 - 2013
25GLUGLUGOLGOL(chain B and (resid 6 through 12 or (resid 13...BB - D3 - 2013
26GLUGLUGOLGOL(chain B and (resid 6 through 12 or (resid 13...BB - D3 - 2013

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Components

#1: Protein tRNA-specific adenosine deaminase 1.14


Mass: 18835.842 Da / Num. of mol.: 2
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: Chemical ChemComp-ZN / ZINC ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: ammonium sulfate, HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.22→56 Å / Num. obs: 23294 / % possible obs: 99.9 % / Redundancy: 14.2 % / CC1/2: 0.999 / Net I/σ(I): 15.2
Reflection shellResolution: 2.22→2.28 Å / Num. unique obs: 1711 / CC1/2: 0.561

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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
Resolution: 2.22→55.21 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2505 1165 5.01 %
Rwork0.216 22069 -
obs0.2178 23234 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.18 Å2 / Biso mean: 64.3384 Å2 / Biso min: 36.03 Å2
Refinement stepCycle: final / Resolution: 2.22→55.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 0 8 38 2224
Biso mean--69.62 63.16 -
Num. residues----291
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A836X-RAY DIFFRACTION6.356TORSIONAL
12B836X-RAY DIFFRACTION6.356TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.22-2.320.31141510.302126832834
2.32-2.440.26831310.253927332864
2.44-2.60.29241330.237727072840
2.6-2.80.28261470.253427162863
2.8-3.080.26351420.221827512893
3.08-3.520.21631420.218327582900
3.52-4.440.22851590.195927752934
4.44-55.210.26331600.209629463106

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