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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Lin, W."

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Search Summary

This query matches 18 Structures.

Refinements

Structure Determination Methodology

experimental (18)

Scientific Name of Source Organism

	Acinetobacter sp. NEB 394 (5)
	Escherichia fergusonii ATCC 35469 (3)
	synthetic construct (3)
	Aquipseudomonas alcaligenes (2)
	Deinococcus wulumuqiensis (2)
	Kinneretia aquatilis (2)
	Salmonella enterica subsp. enterica serovar Typhimurium str. D23580 (2)
	DNA molecule (1)
	Escherichia phage T7 (1)
	Methylophilus methylotrophus (1)

More...

Taxonomy

	Bacteria (18)
	other sequences (3)
	Duplodnaviria (1)
	unclassified sequences (1)

Experimental Method

	X-RAY DIFFRACTION (13)
	ELECTRON MICROSCOPY (5)

Polymer Entity Type

	Protein (18)
	DNA (8)

Refinement Resolution (Å)

	1.5 - 2.0 (2)
	2.0 - 2.5 (5)
	2.5 - 3.0 (4)
	3.0 - 3.5 (3)
	3.5 - 4.0 (4)

Release Date

	2010 - 2014 (2)
	2015 - 2019 (1)
	2020 - 2024 (15)

Enzyme Classification Name

Transferases (5)

Symmetry Type

	Cyclic (12)
	Asymmetric (5)
	Dihedral (3)

AllSelected

1 to 18 of 18 Structures

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Explore in 3D

3LDY \| pdb_00003ldy	Download File View File

An extraordinary mechanism of DNA perturbation exhibited by the rare-cutting HNH restriction endonuclease PacI

Shen, B.W., Heiter, D., Chan, S.-H., Xu, S.-Y., Wilson, G., Stoddard, B.L.

(2010) Structure 18: 734-743

Released	2010-04-21
Method	X-RAY DIFFRACTION 1.97 Å
Organisms	Aquipseudomonas alcaligenes
Macromolecule	restriction endonuclease PacI (protein) DNA (5'-D(GPAPGPGPCPTPTPA)-3') (nucleic acid) DNA (5'-D(PAPTPTPAPAPGPCPCPTPC)-3') (nucleic acid)
Unique Ligands	CA, ZN

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3M7K \| pdb_00003m7k	Download File View File

Crystal structure of PacI-DNA Enzyme product complex

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

(2010) Structure 18: 734-743

Released	2010-04-21
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	Aquipseudomonas alcaligenes
Macromolecule	restriction endonuclease PacI (protein) DNA (5'-D(GPAPGPGPCPTPTPAPAPT)-3') (nucleic acid) DNA (5'-D(PTPAPAPGPCPCPTPC)-3') (nucleic acid)
Unique Ligands	EDO, MG, NA, PT, SO4, ZN

Explore in 3D

5HR4 \| pdb_00005hr4	Download File View File

Structure of Type IIL restriction-modification enzyme MmeI in complex with DNA has implications for engineering of new specificities

Callahan, S.J., Luyten, Y.A., Gupta, Y.K., Wilson, G.G., Roberts, R.J., Morgan, R.D., Aggarwal, A.K.

(2016) PLoS Biol 14: e1002442-e1002442

Released	2016-04-27
Method	X-RAY DIFFRACTION 2.5964 Å
Organisms	Methylophilus methylotrophus
Macromolecule	MmeI (protein) DNA (5'-D(PGPTPTPAPTPGPTPCPGPGPAPTPA)-3') (nucleic acid) DNA (5'-D(PTPAPTPCPCPGPAPCPAPTPAPAPC)-3') (nucleic acid)
Unique Ligands	CA, SFG

Explore in 3D

7DSU \| pdb_00007dsu	Download File View File

Structure of Mod subunit of the Type III restriction-modification enzyme Mbo45V

Ahmed, I., Chouhan, O.P., Gopinath, A., Morgan, R.D., Bhagat, K., Singh, A., Saikrishnan, K.

To be published

Released	2022-01-05
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Mycoplasmopsis bovis
Macromolecule	Mbo45V (protein)
Unique Ligands	EDO, SFG

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7LO5 \| pdb_00007lo5	Download File View File

cryoEM structure DrdV-DNA complex

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

(2021) Structure 29: 521-530.e5

Released	2021-03-17
Method	ELECTRON MICROSCOPY 2.86 Å
Organisms	Deinococcus wulumuqiensis synthetic construct
Macromolecule	Site-specific DNA-methyltransferase (adenine-specific) (protein) DNA (27-MER) (nucleic acid) DNA (28-MER) (nucleic acid)
Unique Ligands	CA, SAM

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7LVV \| pdb_00007lvv	Download File View File

cryoEM structure DrdV-DNA complex

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

(2021) Structure 29: 521-530.e5

Released	2021-03-17
Method	ELECTRON MICROSCOPY 3.25 Å
Organisms	Deinococcus wulumuqiensis synthetic construct
Macromolecule	Site-specific DNA-methyltransferase (adenine-specific) (protein) DNA (27-MER) (nucleic acid) DNA (28-MER) (nucleic acid)
Unique Ligands	CA, SAM

Explore in 3D

7P9K \| pdb_00007p9k	Download File View File

BrxU, GmrSD-family Type IV restriction enzyme

Picton, D.M., Luyten, Y., Morgan, R.D., Nelson, A., Smith, D.L., Dryden, D.T.F., Hinton, J.C.D., Blower, T.R.

(2021) Nucleic Acids Res 49: 11257-11273

Released	2021-12-08
Method	X-RAY DIFFRACTION 2.12 Å
Organisms	Escherichia fergusonii ATCC 35469
Macromolecule	DUF262 domain-containing protein (protein)
Unique Ligands	CL, GOL, SO4

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7P9M \| pdb_00007p9m	Download File View File

BrxU, GmrSD-family Type IV restriction enzyme

Picton, D.M., Luyten, Y., Morgan, R.D., Nelson, A., Smith, D.L., Dryden, D.T.F., Hinton, J.C.D., Blower, T.R.

(2021) Nucleic Acids Res 49: 11257-11273

Released	2021-12-08
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Escherichia fergusonii ATCC 35469
Macromolecule	DUF262 domain-containing protein (protein)
Unique Ligands	CL, SO4

Explore in 3D

7QFZ \| pdb_00007qfz	Download File View File

BrxR, a WYL-domain containing transcriptional regulator

Picton, D.M., Blower, T.R.

(2022) Nucleic Acids Res 50: 5191-5207

Released	2022-05-18
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Escherichia fergusonii ATCC 35469
Macromolecule	WYL domain-containing protein (protein)
Unique Ligands	SO4

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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

Explore in 3D

8C45 \| pdb_00008c45	Download File View File

PglX methyltransferase from the Salmonella BREX phage defence system (aka BrxX)

Blower, T.R., Went, S.C.

(2024) Nat Commun 15: 7236-7236

Released	2024-07-10
Method	X-RAY DIFFRACTION 3.5 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium str. D23580
Macromolecule	site-specific DNA-methyltransferase (adenine-specific) (protein)
Unique Ligands	SAM

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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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8EM1 \| pdb_00008em1	Download File View File

Type IIS Restriction Endonuclease PaqCI, DNA Unbound

Kennedy, M.A., Stoddard, B.L.

(2023) Nucleic Acids Res 51: 4467-4487

Released	2023-03-22
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Kinneretia aquatilis
Macromolecule	PaqCI, DNA Unbound (protein)
Unique Ligands	EDO

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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)

Explore in 3D

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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8EPX \| pdb_00008epx	Download File View File

Type IIS Restriction Endonuclease PaqCI, DNA bound

Kennedy, M.A., Stoddard, B.L.

(2023) Nucleic Acids Res 51: 4467-4487

Released	2023-03-22
Method	ELECTRON MICROSCOPY 3.15 Å
Organisms	DNA molecule Kinneretia aquatilis
Macromolecule	Unique protein chains: 1 Unique nucleic acid chains: 8
Unique Ligands	CA

Explore in 3D

8Q56 \| pdb_00008q56	Download File View File

PglX methyltransferase of Salmonella BREX phage defence system (aka BrxX) bound to inhibitor Ocr

Went, S.C., Blower, T.R.

(2024) Nat Commun 15: 7236-7236

Released	2024-08-21
Method	X-RAY DIFFRACTION 3.5 Å
Organisms	Escherichia phage T7 Salmonella enterica subsp. enterica serovar Typhimurium str. D23580
Macromolecule	Protein Ocr (protein) site-specific DNA-methyltransferase (adenine-specific) (protein)
Unique Ligands	SAM

1 to 18 of 18 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.

3LDY | pdb_00003ldy

An extraordinary mechanism of DNA perturbation exhibited by the rare-cutting HNH restriction endonuclease PacI

3M7K | pdb_00003m7k

Crystal structure of PacI-DNA Enzyme product complex

5HR4 | pdb_00005hr4

Structure of Type IIL restriction-modification enzyme MmeI in complex with DNA has implications for engineering of new specificities

7DSU | pdb_00007dsu

Structure of Mod subunit of the Type III restriction-modification enzyme Mbo45V

7LO5 | pdb_00007lo5

cryoEM structure DrdV-DNA complex

7LVV | pdb_00007lvv

cryoEM structure DrdV-DNA complex

7P9K | pdb_00007p9k

BrxU, GmrSD-family Type IV restriction enzyme

7P9M | pdb_00007p9m

BrxU, GmrSD-family Type IV restriction enzyme

7QFZ | pdb_00007qfz

BrxR, a WYL-domain containing transcriptional regulator

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

8C45 | pdb_00008c45

PglX methyltransferase from the Salmonella BREX phage defence system (aka BrxX)

8EIL | pdb_00008eil

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

8EM1 | pdb_00008em1

Type IIS Restriction Endonuclease PaqCI, DNA Unbound

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

8EPX | pdb_00008epx

Type IIS Restriction Endonuclease PaqCI, DNA bound

8Q56 | pdb_00008q56

PglX methyltransferase of Salmonella BREX phage defence system (aka BrxX) bound to inhibitor Ocr

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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

3LDY | pdb_00003ldy

3M7K | pdb_00003m7k

5HR4 | pdb_00005hr4

7DSU | pdb_00007dsu

7LO5 | pdb_00007lo5

7LVV | pdb_00007lvv

7P9K | pdb_00007p9k

7P9M | pdb_00007p9m

7QFZ | pdb_00007qfz

7T8K | pdb_00007t8k

7T8L | pdb_00007t8l

8C45 | pdb_00008c45

8EIL | pdb_00008eil

8EM1 | pdb_00008em1

8EMC | pdb_00008emc

8EMH | pdb_00008emh

8EPX | pdb_00008epx

8Q56 | pdb_00008q56