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- PDB-8e2p: Crystal structure of TadA*8.20 in a complex with ssDNA -

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Basic information

Entry
Database: PDB / ID: 8e2p
TitleCrystal structure of TadA*8.20 in a complex with ssDNA
Components
  • DNA (5'-D(P*GP*CP*TP*CP*GP*GP*CP*TP*(D8A)P*CP*GP*GP*A)-3')
  • tRNA-specific adenosine deaminase 8.20
KeywordsDNA BINDING PROTEIN/DNA / deaminase / ssDNA / TadA / 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: 2.72 Å
AuthorsFeliciano, P.R. / Lee, S.J. / Ciaramella, G.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
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 8.20
B: tRNA-specific adenosine deaminase 8.20
C: tRNA-specific adenosine deaminase 8.20
D: tRNA-specific adenosine deaminase 8.20
E: DNA (5'-D(P*GP*CP*TP*CP*GP*GP*CP*TP*(D8A)P*CP*GP*GP*A)-3')
F: DNA (5'-D(P*GP*CP*TP*CP*GP*GP*CP*TP*(D8A)P*CP*GP*GP*A)-3')
G: DNA (5'-D(P*GP*CP*TP*CP*GP*GP*CP*TP*(D8A)P*CP*GP*GP*A)-3')
H: DNA (5'-D(P*GP*CP*TP*CP*GP*GP*CP*TP*(D8A)P*CP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,19912
Polymers90,9378
Non-polymers2624
Water39622
1
A: tRNA-specific adenosine deaminase 8.20
B: tRNA-specific adenosine deaminase 8.20
E: DNA (5'-D(P*GP*CP*TP*CP*GP*GP*CP*TP*(D8A)P*CP*GP*GP*A)-3')
F: DNA (5'-D(P*GP*CP*TP*CP*GP*GP*CP*TP*(D8A)P*CP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5996
Polymers45,4694
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-109 kcal/mol
Surface area14470 Å2
MethodPISA
2
C: tRNA-specific adenosine deaminase 8.20
D: tRNA-specific adenosine deaminase 8.20
G: DNA (5'-D(P*GP*CP*TP*CP*GP*GP*CP*TP*(D8A)P*CP*GP*GP*A)-3')
H: DNA (5'-D(P*GP*CP*TP*CP*GP*GP*CP*TP*(D8A)P*CP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5996
Polymers45,4694
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-106 kcal/mol
Surface area14130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.670, 84.670, 214.930
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 20 or (resid 21...
21(chain B and ((resid 6 and (name N or name...
31(chain C and ((resid 6 and (name N or name...
41(chain D and (resid 6 through 19 or (resid 20...
12chain F
22chain G
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
111PHEPHELYSLYS(chain A and (resid 6 through 20 or (resid 21...AA6 - 206 - 20
121ARGARGALAALA(chain A and (resid 6 through 20 or (resid 21...AA21 - 2221 - 22
131PHEPHEPHEPHE(chain A and (resid 6 through 20 or (resid 21...AA6 - 1566 - 156
141PHEPHEPHEPHE(chain A and (resid 6 through 20 or (resid 21...AA6 - 1566 - 156
151PHEPHEPHEPHE(chain A and (resid 6 through 20 or (resid 21...AA6 - 1566 - 156
161PHEPHEPHEPHE(chain A and (resid 6 through 20 or (resid 21...AA6 - 1566 - 156
211PHEPHEPHEPHE(chain B and ((resid 6 and (name N or name...BB66
221GLUGLUPHEPHE(chain B and ((resid 6 and (name N or name...BB3 - 1563 - 156
231GLUGLUPHEPHE(chain B and ((resid 6 and (name N or name...BB3 - 1563 - 156
241GLUGLUPHEPHE(chain B and ((resid 6 and (name N or name...BB3 - 1563 - 156
251GLUGLUPHEPHE(chain B and ((resid 6 and (name N or name...BB3 - 1563 - 156
311PHEPHEPHEPHE(chain C and ((resid 6 and (name N or name...CC66
321VALVALARGARG(chain C and ((resid 6 and (name N or name...CC4 - 1544 - 154
331VALVALARGARG(chain C and ((resid 6 and (name N or name...CC4 - 1544 - 154
341VALVALARGARG(chain C and ((resid 6 and (name N or name...CC4 - 1544 - 154
351VALVALARGARG(chain C and ((resid 6 and (name N or name...CC4 - 1544 - 154
411PHEPHEALAALA(chain D and (resid 6 through 19 or (resid 20...DD6 - 196 - 19
421LYSLYSALAALA(chain D and (resid 6 through 19 or (resid 20...DD20 - 2220 - 22
431PHEPHEPHEPHE(chain D and (resid 6 through 19 or (resid 20...DD6 - 1566 - 156
441PHEPHEPHEPHE(chain D and (resid 6 through 19 or (resid 20...DD6 - 1566 - 156
451PHEPHEPHEPHE(chain D and (resid 6 through 19 or (resid 20...DD6 - 1566 - 156
461PHEPHEPHEPHE(chain D and (resid 6 through 19 or (resid 20...DD6 - 1566 - 156
112DCDCDADAchain FFF4 - 134 - 13
212DCDCDADAchain GGG4 - 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 8.20


Mass: 18737.672 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*TP*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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3,350, ammonium acetate, TRIS pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.97932 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.4
ReflectionResolution: 2.72→43.34 Å / Num. obs: 24824 / % possible obs: 100 % / Redundancy: 10.9 % / CC1/2: 0.995 / Net I/σ(I): 9.4
Reflection shellResolution: 2.72→2.79 Å / Num. unique obs: 1776 / CC1/2: 0.389

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z3A

1z3a


Resolution: 2.72→43.34 Å / Cross valid method: THROUGHOUT / σ(F): 433.42 / Phase error: 33.18 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.218 1155 4.66 %
Rwork0.1901 23618 -
obs0.197 24773 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.51 Å2 / Biso mean: 66.4335 Å2 / Biso min: 45.57 Å2
Refinement stepCycle: final / Resolution: 2.72→43.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4642 909 4 22 5577
Biso mean--58.35 63.77 -
Num. residues----651
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1764X-RAY DIFFRACTION8.47TORSIONAL
12B1764X-RAY DIFFRACTION8.47TORSIONAL
13C1764X-RAY DIFFRACTION8.47TORSIONAL
14D1764X-RAY DIFFRACTION8.47TORSIONAL
21F276X-RAY DIFFRACTION8.47TORSIONAL
22G276X-RAY DIFFRACTION8.47TORSIONAL
23H276X-RAY DIFFRACTION8.47TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.72-2.840.34441470.30382867301495
2.84-2.990.29781660.29982881304795
2.99-3.180.25621510.27332894304595
3.18-3.430.25091340.24362927306196
3.43-3.770.23231420.20872936307895
3.77-4.320.19911680.17572930309895
4.32-5.440.19231230.15633003312696
5.44-43.340.19531240.16733180330496
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)
10.1964-0.12630.12651.8409-1.40171.07170.29140.11740.015-0.882-0.36240.02660.0426-0.09690.23280.88650.15370.09540.5821-0.06950.379335.362317.167616.2648
28.7802-3.02246.50683.2944-0.30826.4906-0.66910.61290.2379-0.2543-0.4141-0.2982-0.4180.76540.34130.68550.21360.24790.5091-0.02560.316932.649620.021121.8973
32.1432-0.831-1.01953.30480.67611.6758-0.09270.15250.0536-0.35170.0370.18490.1193-0.05260.0520.55920.0375-0.04290.3606-0.01150.323227.345922.173227.3703
42.0234-0.7477-0.41972.5035-0.75130.80680.12680.674-0.238-0.6888-0.3210.35130.0445-0.13470.21150.60450.0369-0.09980.5234-0.07910.453721.434711.122120.5827
51.43890.0927-0.41784.5434-2.48184.1638-0.6414-0.1151-0.08260.28030.6752-0.5782-0.2894-0.43760.0470.5490.09990.07590.4815-0.04130.534217.312324.071555.2074
60.83650.0291-0.01834.10491.69151.84450.0212-0.2761-0.1563-0.2482-0.0337-0.0946-0.18330.30570.0330.48260.13070.07150.5157-0.01650.408222.85626.2344.4079
75.2783-3.93480.66085.76781.44965.29550.65960.0064-0.1621-1.3776-0.2558-0.33090.79240.0774-0.42360.66450.11450.0250.47130.11690.410828.942914.383844.2913
82.8719-0.5730.22731.46470.24071.76520.05740.2558-0.2683-0.0186-0.19690.44770.3747-0.2640.15060.4926-0.0696-0.05770.5354-0.01610.530313.024114.681840.8602
91.4489-2.25492.89077.2228-5.05899.1759-0.6474-0.4477-0.24390.07060.7804-0.0452-0.5633-1.7861-0.07020.4788-0.006-0.09050.611-0.06060.51915.619332.579544.8128
101.2844-0.7536-1.35862.8878-1.6484.93030.27120.1354-0.6487-0.2442-0.43240.20190.28240.23630.05530.53190.1456-0.13030.5978-0.04790.641625.915115.759171.7538
113.0731-1.4263-0.1973.2144-1.09060.55260.11330.2236-0.3569-0.14020.0865-0.24080.20490.0371-0.21410.47360.1005-0.07020.56340.00780.362524.260927.86471.2707
125.03011.987-0.65437.90672.8387.0845-0.10780.2897-0.2066-0.1621-0.9255-0.00560.69510.01911.0250.6117-0.0563-0.05680.42830.0820.557816.646828.65970.5474
135.17340.3537-1.77587.4232-2.75919.28220.7129-0.3943-0.7046-0.1529-0.64291.3846-0.44680.7394-0.07260.607-0.0683-0.05870.56140.05680.69785.946626.2173.1754
142.0101-0.4969-0.16922.214-0.70091.01420.0401-0.0208-0.06810.42820.0780.292-0.1932-0.1666-0.13980.4811-0.07230.05790.62550.03220.465117.63524.919281.2263
150.05980.23660.14860.93090.58020.3644-0.46370.0710.21551.18380.49350.2354-0.01370.23660.04851.13280.28990.11280.95620.22340.519521.809526.256790.5935
163.01482.0529-0.39461.4646-0.6191.62210.3017-0.5682-0.20140.2502-0.2096-0.18040.19630.4338-0.11320.60420.0016-0.07870.681-0.00010.459128.291821.498283.3926
170.95630.07570.78451.7623-0.04290.64580.1662-0.2774-0.0999-0.12140.0529-0.3659-0.20370.1372-0.16580.53470.020.12020.6468-0.12580.772711.385153.498277.203
183.14561.8991-0.06435.70910.56632.1729-0.80630.18680.3563-0.22280.94140.28030.04910.5547-0.13280.5076-0.04880.01280.5125-0.06140.540614.731843.142872.6941
193.8394-0.61730.42752.32060.94333.83460.35690.1360.74040.3174-0.2861-0.3117-0.37290.6221-0.01590.4237-0.0954-0.03150.7079-0.02830.594322.205646.783180.7404
208.6468-0.79543.99189.02762.4045.3971-0.33650.1235-0.33151.261-0.446-0.0822-0.2152-0.49340.59670.8986-0.24450.06920.7339-0.08770.268220.741939.190383.1771
211.7714-0.1305-1.68910.4632-0.83523.43170.093-0.58310.3110.27810.08040.0801-0.16960.1206-0.12860.6070.0178-0.01140.6533-0.05810.519113.414345.515189.3897
220.94380.3738-0.30931.0509-0.46530.2310.493-2.76670.35740.8757-0.48310.1742-0.8960.21520.11220.8697-0.19690.14261.6111-0.31810.6482-4.599546.662689.4942
232.9584-1.29562.62823.0275-0.00295.45410.18760.2154-0.76940.0955-0.14010.29450.37710.2399-0.03390.4884-0.07590.00010.49770.00690.57132.9139-5.267530.8463
241.4153-1.9141.05825.0627-0.6173.0480.27940.23230.1135-0.5884-0.21180.44980.40580.0577-0.04790.6438-0.0488-0.05870.59450.01650.56316.916736.143732.6513
255.9286-2.7272-0.32711.92270.39971.8241-0.3751-0.70610.64240.27940.4719-0.69380.17060.0678-0.08930.6432-0.0503-0.09490.6337-0.0640.480540.085834.450184.5289
265.83252.2215-1.08122.23360.11264.04640.7586-0.35540.26910.2199-0.4034-0.3735-0.25470.1222-0.36690.5341-0.08640.03460.71970.03710.5215-5.430335.913383.846
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 24 )A6 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 39 )A25 - 39
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 97 )A40 - 97
4X-RAY DIFFRACTION4chain 'A' and (resid 98 through 156 )A98 - 156
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 24 )B3 - 24
6X-RAY DIFFRACTION6chain 'B' and (resid 25 through 58 )B25 - 58
7X-RAY DIFFRACTION7chain 'B' and (resid 60 through 78 )B60 - 78
8X-RAY DIFFRACTION8chain 'B' and (resid 79 through 137 )B79 - 137
9X-RAY DIFFRACTION9chain 'B' and (resid 138 through 156 )B138 - 156
10X-RAY DIFFRACTION10chain 'C' and (resid 4 through 24 )C4 - 24
11X-RAY DIFFRACTION11chain 'C' and (resid 25 through 57 )C25 - 57
12X-RAY DIFFRACTION12chain 'C' and (resid 58 through 69 )C58 - 69
13X-RAY DIFFRACTION13chain 'C' and (resid 70 through 78 )C70 - 78
14X-RAY DIFFRACTION14chain 'C' and (resid 79 through 104 )C79 - 104
15X-RAY DIFFRACTION15chain 'C' and (resid 105 through 124 )C105 - 124
16X-RAY DIFFRACTION16chain 'C' and (resid 125 through 154 )C125 - 154
17X-RAY DIFFRACTION17chain 'D' and (resid 6 through 39 )D6 - 39
18X-RAY DIFFRACTION18chain 'D' and (resid 40 through 69 )D40 - 69
19X-RAY DIFFRACTION19chain 'D' and (resid 70 through 87 )D70 - 87
20X-RAY DIFFRACTION20chain 'D' and (resid 88 through 97 )D88 - 97
21X-RAY DIFFRACTION21chain 'D' and (resid 98 through 149 )D98 - 149
22X-RAY DIFFRACTION22chain 'D' and (resid 150 through 156 )D150 - 156
23X-RAY DIFFRACTION23chain 'E' and (resid 1 through 13 )E1 - 13
24X-RAY DIFFRACTION24chain 'F' and (resid 4 through 13 )F4 - 13
25X-RAY DIFFRACTION25chain 'G' and (resid 4 through 13 )G4 - 13
26X-RAY DIFFRACTION26chain 'H' and (resid 3 through 13 )H3 - 13

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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