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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Doyle, L.A."

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Search Summary

This query matches 20 Structures.

Refinements

Structure Determination Methodology

experimental (20)

Scientific Name of Source Organism

	synthetic construct (15)
	Acinetobacter sp. NEB 394 (5)
	Saccharomyces cerevisiae (2)
	unidentified (1)

Taxonomy

	other sequences (15)
	Bacteria (5)
	Eukaryota (2)
	unclassified sequences (1)

Experimental Method

	X-RAY DIFFRACTION (17)
	ELECTRON MICROSCOPY (3)

Polymer Entity Type

	Protein (20)
	DNA (2)
	RNA (2)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (2)
	2.0 - 2.5 (12)
	2.5 - 3.0 (1)
	3.0 - 3.5 (1)
	3.5 - 4.0 (2)
	> 4.5 (1)

Release Date

	2015 - 2019 (5)
	2020 - 2024 (15)

Enzyme Classification Name

Isomerases (2)

Symmetry Type

	Asymmetric (11)
	Cyclic (7)
	Dihedral (2)

AllSelected

1 to 20 of 20 Structures

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6CZG \| pdb_00006czg	Download File View File

Structure of a redesigned beta barrel, b11L5F_LGL

Doyle, L.A., Stoddard, B.L.

(2018) Nature 561: 485-491

Released	2018-09-19
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	synthetic construct
Macromolecule	b11L5F_LGL (protein)

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6CZH \| pdb_00006czh	Download File View File

Structure of a redesigned beta barrel, mFAP0, bound to DFHBI

Doyle, L.A., Stoddard, B.L.

(2018) Nature 561: 485-491

Released	2018-09-19
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	synthetic construct
Macromolecule	mFAP0 (protein)
Unique Ligands	38E

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6CZI \| pdb_00006czi	Download File View File

Structure of a redesigned beta barrel, mFAP1, bound to DFHBI

Doyle, L.A., Stoddard, B.L.

(2018) Nature 561: 485-491

Released	2018-09-19
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	synthetic construct
Macromolecule	mFAP1 (protein)
Unique Ligands	38E

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6CZJ \| pdb_00006czj	Download File View File

Structure of a redesigned beta barrel, b10

Doyle, L.A., Stoddard, B.L.

(2018) Nature 561: 485-491

Released	2018-09-19
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	synthetic construct
Macromolecule	b10 (protein)
Unique Ligands	SO4

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6D0T \| pdb_00006d0t	Download File View File

De novo design of a fluorescence-activating beta barrel - BB1

Dou, J., Vorobieva, A.A., Sheffler, W., Doyle, L.A., Park, H., Bick, M.J., Mao, B., Foight, G.W., Lee, M., Carter, L., Sankaran, B., Ovchinnikov, S., Marcos, E., Huang, P., Vaughan, J.C., Stoddard, B.L., Baker, D.

(2018) Nature 561: 485-491

Released	2018-09-19
Method	X-RAY DIFFRACTION 1.63 Å
Organisms	synthetic construct
Macromolecule	BB1 (protein)

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6OHH \| pdb_00006ohh	Download File View File

Structure of EF1p2_mFAP2b bound to DFHBI

Doyle, L.A., Stoddard, B.L.

(2021) Nat Commun 12: 856

Released	2020-04-08
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	synthetic construct
Macromolecule	EF1p2_mFAP2b (protein)
Unique Ligands	38E, CA

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6XR1 \| pdb_00006xr1	Download File View File

Computationally designed right-handed alpha/alpha single-chain toroid with 9 repeats

Hallinan, J.P., Doyle, L., Bradley, P., Stoddard, B.L.

(2021) Commun Biol 4: 1240-1240

Released	2021-07-14
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	synthetic construct
Macromolecule	dTor_9x57R (protein)

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6XR2 \| pdb_00006xr2	Download File View File

Computationally designed right-handed alpha/alpha homotrimeric toroid with 3 repeats per subunit

Hallinan, J.P., Doyle, L., Bradley, P., Stoddard, B.L.

(2021) Commun Biol 4: 1240-1240

Released	2021-07-14
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	synthetic construct
Macromolecule	dTor_3x57R (protein)

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7R9F \| pdb_00007r9f	Download File View File

Wild-type yeast Pseudouridine Synthase, PUS1, bound to 5-Fluorouracil RNA

Doyle, L.A., Stoddard, B.L.

(2023) PLoS One 18: e0291267-e0291267

Released	2021-12-15
Method	X-RAY DIFFRACTION 2.89 Å
Organisms	Saccharomyces cerevisiae synthetic construct
Macromolecule	tRNA pseudouridine synthase 1 (protein) RNA (5'-R(UPAPAPUPCPGPGPGPAPUPUPCPCPGPGPAPUPA)-3') (nucleic acid)
Unique Ligands	SO4

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7R9G \| pdb_00007r9g	Download File View File

Catalytically inactive yeast Pseudouridine Synthase, PUS1, bound to RNA

Doyle, L.A., Stoddard, B.L.

(2023) PLoS One 18: e0291267-e0291267

Released	2021-12-15
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Saccharomyces cerevisiae synthetic construct
Macromolecule	tRNA pseudouridine synthase 1 (protein) RNA (5'-R(APAPAPUPCPGPGPGPAPUPUPCPCPGPGPAPUPA)-3') (nucleic acid)
Unique Ligands	CL, SO4

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7RDR \| pdb_00007rdr	Download File View File

Circular tandem repeat protein with novel repeat topology and enhanced subunit contact surfaces

Shen, B.W., Stoddard, B.L.

(2021) Commun Biol 4: 1240-1240

Released	2021-09-01
Method	ELECTRON MICROSCOPY 6.5 Å
Organisms	unidentified
Macromolecule	Circular tendon repeat protein (protein)

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7SQ3 \| pdb_00007sq3	Download File View File

Designed trefoil knot protein, variant 1

Takushi, B., Doyle, L., Stoddard, B.L., Bradley, P.

(2023) Nat Commun 14: 6746-6746

Released	2022-06-29
Method	X-RAY DIFFRACTION 2.453 Å
Organisms	synthetic construct
Macromolecule	Designed trefoil knot protein, variant 1 (protein)
Unique Ligands	CL, NA

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7SQ4 \| pdb_00007sq4	Download File View File

Designed trefoil knot protein, variant 2

Takushi, B., Doyle, L., Stoddard, B.L., Bradley, P.

(2023) Nat Commun 14: 6746-6746

Released	2022-06-29
Method	X-RAY DIFFRACTION 1.493 Å
Organisms	synthetic construct
Macromolecule	Designed trefoil knot protein, variant 2 (protein)
Unique Ligands	MPD, NA

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7SQ5 \| pdb_00007sq5	Download File View File

Designed trefoil knot protein, variant 3

Takushi, B., Doyle, L., Stoddard, B.L., Bradley, P.

(2023) Nat Commun 14: 6746-6746

Released	2022-11-09
Method	X-RAY DIFFRACTION 2.205 Å
Organisms	synthetic construct
Macromolecule	Designed trefoil knot protein, variant 3 (protein)
Unique Ligands	NA

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7T8K \| pdb_00007t8k	Download File View File

BrxR from Acinetobacter BREX type I phage restriction system bound to DNA

Doyle, L., Kaiser, B., Stoddard, B.

(2022) Nucleic Acids Res 50: 5171-5190

Released	2022-05-18
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Acinetobacter sp. NEB 394
Macromolecule	BrxR (protein) DNA (nucleic acid)
Unique Ligands	CL, EDO

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7T8L \| pdb_00007t8l	Download File View File

BrxR from Acinetobacter BREX type I phage restriction system

Doyle, L., Kaiser, B., Stoddard, B.

(2022) Nucleic Acids Res 50: 5171-5190

Released	2022-05-18
Method	X-RAY DIFFRACTION 2 Å
Organisms	Acinetobacter sp. NEB 394
Macromolecule	BrxR (protein)
Unique Ligands	CL, EDO

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8EIL \| pdb_00008eil	Download File View File

C-Terminal Domain of BrxL from Acinetobacter BREX type I phage restriction system

Doyle, L.A., Stoddard, B.L., Kaiser, B.

(2023) Nucleic Acids Res 51: 3513-3528

Released	2023-02-22
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Acinetobacter sp. NEB 394
Macromolecule	Protease Lon-related BREX system protein BrxL (protein)
Unique Ligands	MLA, SIN

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8EMC \| pdb_00008emc	Download File View File

CryoEM characterization of BrxL -- a unique AAA+ phage restriction Factor.

Shen, B.W., Stoddard, B.L.

(2023) Nucleic Acids Res 51: 3513-3528

Released	2023-02-01
Method	ELECTRON MICROSCOPY 3.6 Å
Organisms	Acinetobacter sp. NEB 394
Macromolecule	Protease Lon-related BREX system protein BrxL (protein)

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8EMH \| pdb_00008emh	Download File View File

CryoEM characterization of a unique AAA+ BrxL phage restriction factor

Shen, B.W., Stoddard, B.L.

(2023) Nucleic Acids Res 51: 3513-3528

Released	2023-02-01
Method	ELECTRON MICROSCOPY 3.63 Å
Organisms	Acinetobacter sp. NEB 394 synthetic construct
Macromolecule	Protease Lon-related BREX system protein BrxL (protein) DNA (63-MER) (nucleic acid) DNA (64-MER) (nucleic acid)

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8ETQ \| pdb_00008etq	Download File View File

Designed pentafoil knot protein folded into a trefoil knot

Doyle, L.A., Kibler, R.D., Bradley, P., Stoddard, B.L.

(2023) Nat Commun 14: 6746-6746

Released	2023-10-25
Method	X-RAY DIFFRACTION 2.42 Å
Organisms	synthetic construct
Macromolecule	k-cTRP5 (protein)

1 to 20 of 20 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

6CZG | pdb_00006czg

Structure of a redesigned beta barrel, b11L5F_LGL

6CZH | pdb_00006czh

Structure of a redesigned beta barrel, mFAP0, bound to DFHBI

6CZI | pdb_00006czi

Structure of a redesigned beta barrel, mFAP1, bound to DFHBI

6CZJ | pdb_00006czj

Structure of a redesigned beta barrel, b10

6D0T | pdb_00006d0t

De novo design of a fluorescence-activating beta barrel - BB1

6OHH | pdb_00006ohh

Structure of EF1p2_mFAP2b bound to DFHBI

6XR1 | pdb_00006xr1

Computationally designed right-handed alpha/alpha single-chain toroid with 9 repeats

6XR2 | pdb_00006xr2

Computationally designed right-handed alpha/alpha homotrimeric toroid with 3 repeats per subunit

7R9F | pdb_00007r9f

Wild-type yeast Pseudouridine Synthase, PUS1, bound to 5-Fluorouracil RNA

7R9G | pdb_00007r9g

Catalytically inactive yeast Pseudouridine Synthase, PUS1, bound to RNA

7RDR | pdb_00007rdr

Circular tandem repeat protein with novel repeat topology and enhanced subunit contact surfaces

7SQ3 | pdb_00007sq3

Designed trefoil knot protein, variant 1

7SQ4 | pdb_00007sq4

Designed trefoil knot protein, variant 2

7SQ5 | pdb_00007sq5

Designed trefoil knot protein, variant 3

7T8K | pdb_00007t8k

BrxR from Acinetobacter BREX type I phage restriction system bound to DNA

7T8L | pdb_00007t8l

BrxR from Acinetobacter BREX type I phage restriction system

8EIL | pdb_00008eil

C-Terminal Domain of BrxL from Acinetobacter BREX type I phage restriction system

8EMC | pdb_00008emc

CryoEM characterization of BrxL -- a unique AAA+ phage restriction Factor.

8EMH | pdb_00008emh

CryoEM characterization of a unique AAA+ BrxL phage restriction factor

8ETQ | pdb_00008etq

Designed pentafoil knot protein folded into a trefoil knot

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

6CZG | pdb_00006czg

6CZH | pdb_00006czh

6CZI | pdb_00006czi

6CZJ | pdb_00006czj

6D0T | pdb_00006d0t

6OHH | pdb_00006ohh

6XR1 | pdb_00006xr1

6XR2 | pdb_00006xr2

7R9F | pdb_00007r9f

7R9G | pdb_00007r9g

7RDR | pdb_00007rdr

7SQ3 | pdb_00007sq3

7SQ4 | pdb_00007sq4

7SQ5 | pdb_00007sq5

7T8K | pdb_00007t8k

7T8L | pdb_00007t8l

8EIL | pdb_00008eil

8EMC | pdb_00008emc

8EMH | pdb_00008emh

8ETQ | pdb_00008etq