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233,249 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Nishioka, T."

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Search Summary

This query matches 22 Structures.

Refinements

Structure Determination Methodology

experimental (22)

Scientific Name of Source Organism

	Pseudonocardia autotrophica (6)
	Priestia megaterium (5)
	Escherichia coli B (3)
	Drosophila melanogaster (2)
	Escherichia coli K-12 (2)
	Escherichia coli (1)
	Rhodococcus erythropolis (1)
	Thermoplasma acidophilum (1)
	Thermoplasma volcanium GSS1 (1)

Taxonomy

	Bacteria (18)
	Archaea (2)
	Eukaryota (2)

Experimental Method

X-RAY DIFFRACTION (22)

Polymer Entity Type

Protein (22)

Refinement Resolution (Å)

	1.5 - 2.0 (2)
	2.0 - 2.5 (14)
	2.5 - 3.0 (4)
	3.0 - 3.5 (2)

Release Date

	1990 - 1994 (1)
	1995 - 1999 (5)
	2005 - 2009 (1)
	2010 - 2014 (15)

Enzyme Classification Name

	Oxidoreductases (13)
	Ligases (6)

Symmetry Type

	Asymmetric (10)
	Dihedral (10)
	Cyclic (3)

SCOP Classification

	All alpha proteins (9)
	Alpha and beta proteins (a/b) (11)
	Artifacts (5)
	Alpha and beta proteins (a+b) (6)

AllSelected

1 to 22 of 22 Structures

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11AS \| pdb_000011as	Download File View File

ASPARAGINE SYNTHETASE MUTANT C51A, C315A COMPLEXED WITH L-ASPARAGINE

Nakatsu, T., Kato, H., Oda, J.

(1998) Nat Struct Biol 5: 15-19

Released	1998-12-30
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli K-12
Macromolecule	ASPARAGINE SYNTHETASE (protein)
Unique Ligands	ASN

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12AS \| pdb_000012as	Download File View File

ASPARAGINE SYNTHETASE MUTANT C51A, C315A COMPLEXED WITH L-ASPARAGINE AND AMP

Nakatsu, T., Kato, H., Oda, J.

(1998) Nat Struct Biol 5: 15-19

Released	1998-12-30
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Escherichia coli K-12
Macromolecule	ASPARAGINE SYNTHETASE (protein)
Unique Ligands	AMP, ASN

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1GLV \| pdb_00001glv	Download File View File

THREE-DIMENSIONAL STRUCTURE OF THE GLUTATHIONE SYNTHETASE FROM ESCHERICHIA COLI B AT 2.0 ANGSTROMS RESOLUTION

Yamaguchi, H., Kato, H., Tanaka, T., Katsube, Y.

(1993) J Mol Biology 229: 1083-1100

Released	1994-01-31
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Escherichia coli
Macromolecule	GLUTATHIONE SYNTHASE (protein)

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1GSA \| pdb_00001gsa	Download File View File

STRUCTURE OF GLUTATHIONE SYNTHETASE COMPLEXED WITH ADP AND GLUTATHIONE

Hara, T., Kato, H., Nishioka, T., Katsube, Y., Oda, J.

(1996) Biochemistry 35: 11967-11974

Released	1996-06-20
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli B
Macromolecule	GLUTATHIONE SYNTHETASE (protein)
Unique Ligands	ADP, GSH, MG, SO4

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1GSH \| pdb_00001gsh	Download File View File

STRUCTURE OF ESCHERICHIA COLI GLUTATHIONE SYNTHETASE AT PH 7.5

Matsuda, K., Kato, H., Yamaguchi, H., Nishioka, T., Katsube, Y., Oda, J.

(1996) Protein Eng 9: 1083-1092

Released	1996-07-11
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli B
Macromolecule	GLUTATHIONE BIOSYNTHETIC LIGASE (protein)

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2GLT \| pdb_00002glt	Download File View File

STRUCTURE OF ESCHERICHIA COLI GLUTATHIONE SYNTHETASE AT PH 6.0.

Matsuda, K., Yamaguchi, H., Kato, H., Nishioka, T., Katsube, Y., Oda, J.

(1996) Protein Eng 9: 1083-1092

Released	1995-07-31
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Escherichia coli B
Macromolecule	GLUTATHIONE BIOSYNTHETIC LIGASE (protein)

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2ZK7 \| pdb_00002zk7	Download File View File

Structure of a C-terminal deletion mutant of Thermoplasma acidophilum aldohexose dehydrogenase (AldT)

Nishioka, T., Yasutake, Y., Nishiya, Y., Tamura, N., Tamura, T.

(2009) Proteins 74: 801-807

Released	2009-01-13
Method	X-RAY DIFFRACTION 2.71 Å
Organisms	Thermoplasma acidophilum
Macromolecule	Glucose 1-dehydrogenase related protein (protein)

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3A4G \| pdb_00003a4g	Download File View File

Structure of cytochrome P450 vdh from Pseudonocardia autotrophica (trigonal crystal form)

Yasutake, Y., Fujii, Y., Cheon, W.K., Arisawa, A., Tamura, T.

(2010) J Biological Chem 285: 31193-31201

Released	2010-07-14
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Pseudonocardia autotrophica
Macromolecule	Vitamin D hydroxylase (protein)
Unique Ligands	HEM, PG0

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3A4H \| pdb_00003a4h	Download File View File

Structure of cytochrome P450 vdh from Pseudonocardia autotrophica (orthorhombic crystal form)

Yasutake, Y., Fujii, Y., Cheon, W.K., Arisawa, A., Tamura, T.

(2010) J Biological Chem 285: 31193-31201

Released	2010-07-14
Method	X-RAY DIFFRACTION 3.06 Å
Organisms	Pseudonocardia autotrophica
Macromolecule	Vitamin D hydroxylase (protein)
Unique Ligands	CA, HEM

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3A4Z \| pdb_00003a4z	Download File View File

Structure of cytochrome P450 Vdh mutant (Vdh-K1) obtained by directed evolution

Yasutake, Y., Fujii, Y., Cheon, W.K., Arisawa, A., Tamura, T.

(2010) J Biological Chem 285: 31193-31201

Released	2010-07-28
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Pseudonocardia autotrophica
Macromolecule	Vitamin D hydroxylase (protein)
Unique Ligands	ACT, CA, GOL, HEM

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3A50 \| pdb_00003a50	Download File View File

Structure of cytochrome P450 Vdh mutant (Vdh-K1) obtained by directed evolution with bound vitamin D3

Yasutake, Y., Fujii, Y., Cheon, W.K., Arisawa, A., Tamura, T.

(2010) J Biological Chem 285: 31193-31201

Released	2010-07-28
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Pseudonocardia autotrophica
Macromolecule	Vitamin D hydroxylase (protein)
Unique Ligands	ACT, CA, GOL, HEM, VD3

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3A51 \| pdb_00003a51	Download File View File

Structure of cytochrome P450 Vdh mutant (Vdh-K1) obtained by directed evolution with bound 25-hydroxyvitamin D3

Yasutake, Y., Fujii, Y., Cheon, W.K., Arisawa, A., Tamura, T.

(2010) J Biological Chem 285: 31193-31201

Released	2010-07-28
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pseudonocardia autotrophica
Macromolecule	Vitamin D hydroxylase (protein)
Unique Ligands	ACT, CA, GOL, HEM, VDY

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3AUS \| pdb_00003aus	Download File View File

Crystal structure of Bacillus megaterium glucose dehydrogenase 4 in ligand-free form

Nishioka, T., Yasutake, Y., Nishiya, Y., Tamura, T.

(2012) FEBS J 279: 3264-3275

Released	2012-02-22
Method	X-RAY DIFFRACTION 2 Å
Organisms	Priestia megaterium
Macromolecule	Glucose 1-dehydrogenase 4 (protein)

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3AUT \| pdb_00003aut	Download File View File

Crystal structure of Bacillus megaterium glucose dehydrogenase 4 in complex with NADH

Nishioka, T., Yasutake, Y., Nishiya, Y., Tamura, T.

(2012) FEBS J 279: 3264-3275

Released	2012-02-22
Method	X-RAY DIFFRACTION 2 Å
Organisms	Priestia megaterium
Macromolecule	Glucose 1-dehydrogenase 4 (protein)
Unique Ligands	NAI

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3AUU \| pdb_00003auu	Download File View File

Crystal structure of Bacillus megaterium glucose dehydrogenase 4 in complex with D-glucose

Nishioka, T., Yasutake, Y., Nishiya, Y., Tamura, T.

(2012) FEBS J 279: 3264-3275

Released	2012-02-22
Method	X-RAY DIFFRACTION 2 Å
Organisms	Priestia megaterium
Macromolecule	Glucose 1-dehydrogenase 4 (protein)
Unique Ligands	BGC

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3AY6 \| pdb_00003ay6	Download File View File

Crystal structure of Bacillus megaterium glucose dehydrogenase 4 A258F mutant in complex with NADH and D-glucose

Nishioka, T., Yasutake, Y., Nishiya, Y., Tamura, T.

(2012) FEBS J 279: 3264-3275

Released	2012-05-23
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Priestia megaterium
Macromolecule	Glucose 1-dehydrogenase 4 (protein)
Unique Ligands	BGC, CL, NAI

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3AY7 \| pdb_00003ay7	Download File View File

Crystal structure of Bacillus megaterium glucose dehydrogenase 4 G259A mutant

Nishioka, T., Yasutake, Y., Nishiya, Y., Tamura, T.

(2012) FEBS J 279: 3264-3275

Released	2012-05-23
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Priestia megaterium
Macromolecule	Glucose 1-dehydrogenase 4 (protein)
Unique Ligands	CL

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3TXM \| pdb_00003txm	Download File View File

Crystal structure of Rpn6 from Drosophila melanogaster, Gd(3+) complex

Pathare, G.R., Bracher, A.

(2012) Proc Natl Acad Sci U S A 109: 149-154

Released	2011-12-14
Method	X-RAY DIFFRACTION 3 Å
Organisms	Drosophila melanogaster
Macromolecule	26S proteasome regulatory complex subunit p42B (protein)
Unique Ligands	GD3, SO4

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3TXN \| pdb_00003txn	Download File View File

Crystal structure of Rpn6 from Drosophila melanogaster, native data

Pathare, G.R., Bracher, A.

(2012) Proc Natl Acad Sci U S A 109: 149-154

Released	2011-12-14
Method	X-RAY DIFFRACTION 2.496 Å
Organisms	Drosophila melanogaster
Macromolecule	26S proteasome regulatory complex subunit p42B (protein)
Unique Ligands	GOL, SO4

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3VRM \| pdb_00003vrm	Download File View File

Structure of cytochrome P450 Vdh mutant T107A with bound vitamin D3

Nishioka, T., Yasutake, Y., Tamura, T.

(2013) Chembiochem 14: 2284-2291

Released	2013-04-17
Method	X-RAY DIFFRACTION 2.57 Å
Organisms	Pseudonocardia autotrophica
Macromolecule	Vitamin D(3) 25-hydroxylase (protein)
Unique Ligands	HEM, VD3