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232,059 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Shimizu, S."

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Search Summary

This query matches 25 Structures.

Refinements

Structure Determination Methodology

experimental (25)

Scientific Name of Source Organism

	Alcaligenes faecalis (3)
	Candida parapsilosis (3)
	Aeromonas jandaei (2)
	Aeropyrum pernix (2)
	Bacillus sp. (in: firmicutes) (2)
	Kluyveromyces marxianus (2)
	Agrobacterium tumefaciens (1)
	Chlamydomonas reinhardtii (1)
	Escherichia coli K-12 (1)
	Homo sapiens (1)

More...

Taxonomy

	Bacteria (9)
	Eukaryota (8)
	Archaea (2)

Experimental Method

X-RAY DIFFRACTION (25)

Polymer Entity Type

	Protein (19)
	DNA (6)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.5 - 2.0 (8)
	2.0 - 2.5 (8)
	2.5 - 3.0 (7)
	3.0 - 3.5 (1)

Release Date

	2000 - 2004 (2)
	2005 - 2009 (4)
	2010 - 2014 (16)
	2015 - 2019 (3)

Enzyme Classification Name

	Oxidoreductases (6)
	Lyases (4)
	Hydrolases (2)
	Ligases (2)
	Isomerases (1)

Symmetry Type

	Asymmetric (7)
	Cyclic (7)
	Dihedral (7)

SCOP Classification

	Alpha and beta proteins (a/b) (12)
	All alpha proteins (2)
	All beta proteins (1)

AllSelected

1 to 25 of 25 Structures

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1V5C	Download File View File

The crystal structure of the inactive form chitosanase from Bacillus sp. K17 at pH3.7

Adachi, W., Shimizu, S., Sunami, T., Fukazawa, T., Suzuki, M., Yatsunami, R., Nakamura, S., Takenaka, A.

(2004) J Mol Biol 343: 785-795

Released	2004-12-07
Method	X-RAY DIFFRACTION 2 Å
Organisms	Bacillus sp. (in: firmicutes)
Macromolecule	chitosanase (protein)
Unique Ligands	SO4

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1V5D	Download File View File

The crystal structure of the active form chitosanase from Bacillus sp. K17 at pH6.4

Adachi, W., Shimizu, S., Sunami, T., Fukazawa, T., Suzuki, M., Yatsunami, R., Nakamura, S., Takenaka, A.

(2004) J Mol Biol 343: 785-795

Released	2004-12-07
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Bacillus sp. (in: firmicutes)
Macromolecule	chitosanase (protein)
Unique Ligands	PIN

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2YZ7	Download File View File

X-ray analyses of 3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis

Hoque, M.M., Juan, E.C.M., Shimizu, S., Hossain, M.T., Takenaka, A.

(2008) Acta Crystallogr D Biol Crystallogr 64: 496-505

Released	2008-04-22
Method	X-RAY DIFFRACTION 2.19 Å
Organisms	Alcaligenes faecalis
Macromolecule	D-3-hydroxybutyrate dehydrogenase (protein)
Unique Ligands	CA, CL

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2Z6W	Download File View File

Crystal structure of human cyclophilin D in complex with cyclosporin A

Kajitani, K., Fujihashi, M., Kobayashi, Y., Shimizu, S., Tsujimoto, Y., Miki, K.

(2008) Proteins 70: 1635

Released	2008-04-29
Method	X-RAY DIFFRACTION 0.96 Å
Organisms	Homo sapiens Tolypocladium inflatum
Macromolecule	CYCLOSPORIN A (protein) PEPTIDYL-PROLYL CIS-TRANS ISOMERASE (protein)
Unique Ligands	CIT

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3A31	Download File View File

Crystal structure of putative threonyl-tRNA synthetase ThrRS-1 from Aeropyrum pernix (selenomethionine derivative)

Shimizu, S., Juan, E.C.M., Miyashita, Y., Sato, Y., Hoque, M.M., Suzuki, K., Yogiashi, M., Tsunoda, M., Dock-Bregeon, A.-C., Moras, D., Sekiguchi, T., Takenaka, A.

(2009) J Mol Biol 394: 286-296

Released	2009-10-27
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Aeropyrum pernix
Macromolecule	Probable threonyl-tRNA synthetase 1 (protein)
Unique Ligands	SO4, ZN

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3A32	Download File View File

Crystal structure of putative threonyl-tRNA synthetase ThrRS-1 from Aeropyrum pernix

Shimizu, S., Juan, E.C.M., Miyashita, Y., Sato, Y., Hoque, M.M., Suzuki, K., Yogiashi, M., Tsunoda, M., Dock-Bregeon, A.-C., Moras, D., Sekiguchi, T., Takenaka, A.

(2009) J Mol Biol 394: 286-296

Released	2009-10-27
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Aeropyrum pernix
Macromolecule	Probable threonyl-tRNA synthetase 1 (protein)
Unique Ligands	SO4, ZN

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3AK4	Download File View File

Crystal structure of NADH-dependent quinuclidinone reductase from agrobacterium tumefaciens

Miyakawa, T., Kataoka, M., Takeshita, D., Nomoto, F., Nagata, K., Shimizu, S., Tanokura, M.

To be published

Released	2011-07-13
Method	X-RAY DIFFRACTION 2 Å
Organisms	Agrobacterium tumefaciens
Macromolecule	NADH-dependent quinuclidinone reductase (protein)
Unique Ligands	NAD

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3B1B	Download File View File

The unique structure of wild type carbonic anhydrase alpha-CA1 from Chlamydomonas reinhardtii

Shimizu, S., Takenaka, A.

(2011) Acta Crystallogr D Biol Crystallogr 67: 894-901

Released	2011-11-16
Method	X-RAY DIFFRACTION 1.88 Å
Organisms	Chlamydomonas reinhardtii
Macromolecule	Carbonic anhydrase 1 (protein)
Unique Ligands	NAG, SO4, ZN

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3GJH	Download File View File

Crystal structure of a DNA duplex containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one

Takenaka, A., Juan, E.C.M., Shimizu, S., Haraguchi, T., Xiao, M., Kurose, T.

To be published

Released	2010-03-31
Method	X-RAY DIFFRACTION 2.9 Å
Macromolecule	5'-D(CPGPCPGPAPAPTPTP(B7C)PGPCPG)-3' (nucleic acid)
Unique Ligands	DAP

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3GJJ	Download File View File

crystal structure of a DNA duplex containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one

Takenaka, A., Juan, E.C.M., Shimizu, S., Haraguchi, T., Xiao, M., Kurose, T., Ohkubo, A., Sekine, M., Shibata, T., Millington, C.L., Williams, D.M.

To be published

Released	2010-03-31
Method	X-RAY DIFFRACTION 2.9 Å
Macromolecule	5'-D(CPGPCPGPAPAPTP(B7C)PCPGPCPG)-3' (nucleic acid)
Unique Ligands	HT

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3GJK	Download File View File

crystal structure of a DNA duplex containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one

Takenaka, A., Juan, E.C.M., Shimizu, S., Haraguchi, T., Xiao, M., Kurose, T., Ohkubo, A., Sekine, M., Shibata, T., Millington, C.L., Williams, D.M.

To be published

Released	2010-03-31
Method	X-RAY DIFFRACTION 2.2 Å
Macromolecule	5'-D(CPGPCPGPAPA)-3' (nucleic acid) 5'-D(PTPTP(B7C)PGPCPG)-3' (nucleic acid)
Unique Ligands	K

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3GJL	Download File View File

crystal structure of a DNA duplex containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one

Takenaka, A., Juan, E.C.M., Shimizu, S., Haraguchi, T., Xiao, M., Kurose, T., Ohkubo, A., Sekine, M., Shibata, T., Millington, C.L., Williams, D.M.

To be published

Released	2010-03-31
Method	X-RAY DIFFRACTION 1.92 Å
Macromolecule	5'-D(CPGPCPGPAPA)-3' (nucleic acid) 5'-D(PTPTP(B7C)PGPCPG)-3' (nucleic acid)
Unique Ligands	NA

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3N4N	Download File View File

Insights into the stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido[2,3-d]pyrimidin-2-one

Takenaka, A., Juan, E.C.M., Shimizu, S.

(2010) Nucleic Acids Res

Released	2010-08-11
Method	X-RAY DIFFRACTION 1.92 Å
Macromolecule	5'-D(CPGPCPGPAPA)-3' (nucleic acid) 5'-D(PTPTP(B7C)PGPCPG)-3' (nucleic acid)

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3N4O	Download File View File

Insights into the stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido[2,3-d]pyrimidin-2-one

Takenaka, A., Juan, E.C.M., Shimizu, S.

(2010) Nucleic Acids Res

Released	2010-08-11
Method	X-RAY DIFFRACTION 2.9 Å
Macromolecule	5'-D(CPGPCPGPAPAPTP(B7C)PCPGPCPG)-3' (nucleic acid)
Unique Ligands	HT

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3VDQ	Download File View File

Crystal structure of alcaligenes faecalis D-3-hydroxybutyrate dehydrogenase in complex with NAD(+) and acetate

Hoque, M.M., Shimizu, S., Hossain, M.T., Yamamoto, T., Suzuki, K., Takenaka, A.

(2008) Acta Crystallogr D Biol Crystallogr 64: 496-505

Released	2012-02-29
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Alcaligenes faecalis
Macromolecule	D-3-hydroxybutyrate dehydrogenase (protein)
Unique Ligands	ACT, CA, CL, NAD

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3VDR	Download File View File

Crystal structure of D-3-hydroxybutyrate dehydrogenase, prepared in the presence of the substrate D-3-hydroxybutyrate and NAD(+)

Hoque, M.M., Shimizu, S., Juan, E.C.M., Sato, Y., Hossain, M.T., Yamamoto, T., Imamura, S., Amano, H., Suzuki, K., Sekiguchi, T., Tsunoda, M., Takenaka, A.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 331-335

Released	2012-02-08
Method	X-RAY DIFFRACTION 3 Å
Organisms	Alcaligenes faecalis
Macromolecule	D-3-hydroxybutyrate dehydrogenase (protein)
Unique Ligands	3HR, AAE, CA, CL, NAD, NAI

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3VXG	Download File View File

Crystal structure of conjugated polyketone reductase C2 from Candida Parapsilosis

Qin, H.-M., Yamamura, A., Miyakawa, T., Maruoka, S., Ohtsuka, J., Nagata, K., Kataoka, M., Shimizu, S., Tanokura, M.

(2014) Appl Microbiol Biotechnol 98: 243-249

Released	2013-08-07
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Candida parapsilosis
Macromolecule	Conjugated polyketone reductase C2 (protein)

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3WG6	Download File View File

Crystal structure of conjugated polyketone reductase C1 from Candida parapsilosis complexed with NADPH

Qin, H.-M., Yamamura, A., Miyakawa, T., Maruoka, S., Ohtsuka, J., Nagata, K., Kataoka, M., Shimizu, S., Tanokura, M.

(2013) Proteins 81: 2059-2063

Released	2013-08-21
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Candida parapsilosis
Macromolecule	Conjugated polyketone reductase C1 (protein)
Unique Ligands	NDP

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3WGB	Download File View File

Crystal structure of aeromonas jandaei L-allo-threonine aldolase

Qin, H.M., Imai, F.L., Miyakawa, T., Kataoka, M., Okai, M., Ohtsuka, J., Hou, F., Nagata, K., Shimizu, S., Tanokura, M.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1695-1703

Released	2014-07-09
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Aeromonas jandaei
Macromolecule	L-allo-threonine aldolase (protein)
Unique Ligands	GLY, PLG

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3WGC	Download File View File

Aeromonas jandaei L-allo-threonine aldolase H128Y/S292R double mutant

Qin, H.M., Imai, F.L., Miyakawa, T., Kataoka, M., Okai, M., Ohtsuka, J., Hou, F., Nagata, K., Shimizu, S., Tanokura, M.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1695-1703

Released	2014-07-09
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Aeromonas jandaei
Macromolecule	L-allo-threonine aldolase (protein)
Unique Ligands	PLG

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3WLX	Download File View File

Crystal structure of low-specificity L-threonine aldolase from Escherichia coli

Qin, H.-M., Imai, F.L., Miyakawa, T., Kataoka, M., Okai, M., Hou, F., Ohtsuka, J., Nagata, K., Shimizu, S., Tanokura, M.

To be published

Released	2014-12-17
Method	X-RAY DIFFRACTION 2.51 Å
Organisms	Escherichia coli K-12
Macromolecule	Low specificity L-threonine aldolase (protein)
Unique Ligands	PLG

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4H8N	Download File View File

Crystal structure of conjugated polyketone reductase C2 from candida parapsilosis complexed with NADPH

Qin, H.-M., Yamamura, A., Miyakawa, T., Maruoka, S., Ohtsuka, J., Nagata, K., Kataoka, M., Shimizu, S., Tanokura, M.

(2014) Appl Microbiol Biotechnol 98: 243-249

Released	2013-08-07
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Candida parapsilosis
Macromolecule	Conjugated polyketone reductase C2 (protein)
Unique Ligands	NDP

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4TMB	Download File View File

CRYSTAL STRUCTURE of OLD YELLOW ENZYME from CANDIDA MACEDONIENSIS AKU4588

Horita, S., Kataoka, M., Kitamura, N., Nakagawa, T., Miyakawa, T., Ohtsuka, J., Nagata, K., Shimizu, S., Tanokura, M.

(2015) Chembiochem 16: 440-445

Released	2015-02-11
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Kluyveromyces marxianus
Macromolecule	Old yellow enzyme (protein)
Unique Ligands	FMN

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4TMC	Download File View File

CRYSTAL STRUCTURE of OLD YELLOW ENZYME from CANDIDA MACEDONIENSIS AKU4588 COMPLEXED with P-HYDROXYBENZALDEHYDE

Horita, S., Kataoka, M., Kitamura, N., Nakagawa, T., Miyakawa, T., Ohtsuka, J., Nagata, K., Shimizu, S., Tanokura, M.

(2015) Chembiochem 16: 440-445

Released	2015-02-11
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Kluyveromyces marxianus
Macromolecule	Old yellow enzyme (protein)
Unique Ligands	FMN, HBA

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6AGZ	Download File View File

Crystal structure of Old Yellow Enzyme from Pichia sp. AKU4542

Horita, S., Kataoka, M., Kitamura, N., Nakagawa, T., Miyakawa, T., Ohtsuka, J., Nagata, K., Shimizu, S., Tanokura, M.

(2019) Biosci Biotechnol Biochem 83: 456-462

Released	2019-06-26
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pichia
Macromolecule	Old Yellow Enzyme (protein)
Unique Ligands	FMN

1 to 25 of 25 Structures

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