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235,183 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Shimizu-Ibuka, A."

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Search Summary

This query matches 11 Structures.

Refinements

Structure Determination Methodology

experimental (11)

Scientific Name of Source Organism

	Klebsiella pneumoniae (4)
	Pseudomonas aeruginosa (2)
	Escherichia coli (1)
	Latilactobacillus sakei (1)
	Molineria latifolia (1)
	Morganella morganii (1)
	Vitis vinifera (1)

Taxonomy

	Bacteria (9)
	Eukaryota (2)

Experimental Method

X-RAY DIFFRACTION (11)

Polymer Entity Type

Protein (11)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (5)
	2.0 - 2.5 (4)
	2.5 - 3.0 (1)

Release Date

	2005 - 2009 (3)
	2010 - 2014 (1)
	2015 - 2019 (4)
	2020 - 2024 (3)

Enzyme Classification Name

	Hydrolases (7)
	Isomerases (1)

Symmetry Type

	Asymmetric (9)
	Cyclic (2)

SCOP Classification

	All beta proteins (2)
	Multi-domain proteins (alpha and beta) (5)
	Alpha and beta proteins (a+b) (2)

AllSelected

1 to 11 of 11 Structures

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1WE4 \| pdb_00001we4	Download File View File

Crystal Structure of Class A beta-Lactamase Toho-1 G238C mutant

Shimizu-Ibuka, A., Matsuzawa, H., Sakai, H.

(2004) Biochemistry 43: 15737-15745

Released	2005-03-15
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Escherichia coli
Macromolecule	Beta-lactamase Toho-1 (protein)
Unique Ligands	SO4

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2D04 \| pdb_00002d04	Download File View File

Crystal structure of neoculin, a sweet protein with taste-modifying activity.

Shimizu-Ibuka, A., Morita, Y., Terada, T., Asakura, T., Nakajima, K., Iwata, S., Misaka, T., Sorimachi, H., Arai, S., Abe, K.

(2006) J Mol Biology 359: 148-158

Released	2006-06-20
Method	X-RAY DIFFRACTION 2.76 Å
Organisms	Molineria latifolia
Macromolecule	Curculin (protein) neoculin acidic subunit (protein)
Unique Ligands	NAG
Unique branched monosaccharides	BMA, FUL, NAG

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2ZC7 \| pdb_00002zc7	Download File View File

Crystal Structure of Class C beta-Lactamase ACT-1

Shimizu-Ibuka, A., Sakai, H., Galleni, M.

(2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 334-337

Released	2008-09-23
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Beta-lactamase ACT-1 (protein)

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3W8K \| pdb_00003w8k	Download File View File

Crystal structure of class C beta-lactamase Mox-1

Shimizu-ibuka, A., Oguri, T., Furuyama, T., Ishii, Y.

(2014) Antimicrob Agents Chemother 58: 3914-3920

Released	2014-04-23
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Beta-lactamase (protein)
Unique Ligands	ACT, ZN

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4WBG \| pdb_00004wbg	Download File View File

Crystal structure of class C beta-lactamase Mox-1 covalently complexed with aztorenam

Oguri, T., Shimizu-ibuka, A., Ishii, Y.

(2015) Antimicrob Agents Chemother 59: 5069-5072

Released	2015-07-01
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Beta-lactamase (protein)
Unique Ligands	ACT, AZR, ZN

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5B3R \| pdb_00005b3r	Download File View File

Crystal structure of metallo-beta-lactamase IMP-18 from Pseudomonas aeruginosa

Shimizu-Ibuka, A., Ishii, Y.

(2016) Antimicrob Agents Chemother 60: 5521-5526

Released	2017-02-15
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	IMP-18 (protein)
Unique Ligands	CIT, ZN

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5YH4 \| pdb_00005yh4	Download File View File

Miraculin-like protein from Vitis vinifera

Shimizu-Ibuka, A., Furukawa, N.

(2018) Biochim Biophys Acta Proteins Proteom 1866: 1125-1130

Released	2018-10-03
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Vitis vinifera
Macromolecule	mirauclin-like protein (protein)
Unique Ligands	EDO

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5ZYB \| pdb_00005zyb	Download File View File

Crystal structure of MOX-1 complexed with a boronic acid transition state inhibitor S02030

Shimizu-Ibuka, A., Furukawa, N.

To be published

Released	2019-06-26
Method	X-RAY DIFFRACTION 2.13 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Beta-lactamase (protein)
Unique Ligands	ACT, ZN, ZXM

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6L3S \| pdb_00006l3s	Download File View File

Crystal structure of metallo-beta-lactamase IMP-27 from Morganella morganii

Kato, Y., Shimizu-Ibuka, A.

To be published

Released	2020-10-28
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Morganella morganii
Macromolecule	IMP-27 metallo-beta-lactamase (protein)
Unique Ligands	ZN

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7XLL \| pdb_00007xll	Download File View File

Alanine racemase from Lactobacillus sakei Uonuma-1.

Shimizu-Ibuka, A., Kato, Y.

(2023) FEBS J 290: 2954-2967

Released	2023-03-01
Method	X-RAY DIFFRACTION 1.76 Å
Organisms	Latilactobacillus sakei
Macromolecule	Alanine racemase (protein)
Unique Ligands	ACT, ALA, PEG

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7YRP \| pdb_00007yrp	Download File View File

Crystal structure of VIM-28 metallo-beta-lactamase

Shimizu-Ibuka, A., Sato, H.

To be published

Released	2023-06-21
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	Metallo-beta-lactamase VIM-28 (protein)
Unique Ligands	FLC, GOL, ZN

1 to 11 of 11 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.

1WE4 | pdb_00001we4

Crystal Structure of Class A beta-Lactamase Toho-1 G238C mutant

2D04 | pdb_00002d04

Crystal structure of neoculin, a sweet protein with taste-modifying activity.

2ZC7 | pdb_00002zc7

Crystal Structure of Class C beta-Lactamase ACT-1

3W8K | pdb_00003w8k

Crystal structure of class C beta-lactamase Mox-1

4WBG | pdb_00004wbg

Crystal structure of class C beta-lactamase Mox-1 covalently complexed with aztorenam

5B3R | pdb_00005b3r

Crystal structure of metallo-beta-lactamase IMP-18 from Pseudomonas aeruginosa

5YH4 | pdb_00005yh4

Miraculin-like protein from Vitis vinifera

5ZYB | pdb_00005zyb

Crystal structure of MOX-1 complexed with a boronic acid transition state inhibitor S02030

6L3S | pdb_00006l3s

Crystal structure of metallo-beta-lactamase IMP-27 from Morganella morganii

7XLL | pdb_00007xll

Alanine racemase from Lactobacillus sakei Uonuma-1.

7YRP | pdb_00007yrp

Crystal structure of VIM-28 metallo-beta-lactamase

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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

SCOP Classification

1WE4 | pdb_00001we4

2D04 | pdb_00002d04

2ZC7 | pdb_00002zc7

3W8K | pdb_00003w8k

4WBG | pdb_00004wbg

5B3R | pdb_00005b3r

5YH4 | pdb_00005yh4

5ZYB | pdb_00005zyb

6L3S | pdb_00006l3s

7XLL | pdb_00007xll

7YRP | pdb_00007yrp