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235,183 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Kitamura, M."

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Search Summary

This query matches 22 Structures.

Refinements

Structure Determination Methodology

experimental (22)

Scientific Name of Source Organism

	Nitratidesulfovibrio vulgaris str. 'Miyazaki F (11)
	Bacteroides thetaiotaomicron (2)
	Pseudomonas aeruginosa PAO1 (2)
	Bacteroides thetaiotaomicron VPI-5482 (1)
	Escherichia coli (1)
	Homo sapiens (1)
	Lactococcus lactis subsp. lactis Il1403 (1)
	Nitratidesulfovibrio vulgaris (1)
	Nitratidesulfovibrio vulgaris str. Hildenborough (1)
	Nostoc punctiforme NIES-2108 (1)

Taxonomy

	Bacteria (21)
	Eukaryota (1)

Experimental Method

X-RAY DIFFRACTION (22)

Polymer Entity Type

Protein (22)

Refinement Resolution (Å)

	1.0 - 1.5 (4)
	1.5 - 2.0 (9)
	2.0 - 2.5 (6)
	2.5 - 3.0 (1)
	3.0 - 3.5 (2)

Release Date

	2000 - 2004 (1)
	2005 - 2009 (6)
	2010 - 2014 (10)
	2015 - 2019 (3)
	2020 - 2024 (2)

Enzyme Classification Name

	Hydrolases (4)
	Oxidoreductases (1)
	Transferases (1)

Symmetry Type

	Cyclic (16)
	Asymmetric (7)
	Dihedral (1)

SCOP Classification

	All beta proteins (6)
	Alpha and beta proteins (a/b) (3)
	All alpha proteins (2)
	Alpha and beta proteins (a+b) (1)

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1 to 22 of 22 Structures

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1FLM \| pdb_00001flm	Download File View File

DIMER OF FMN-BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS (MIYAZAKI F)

Suto, K., Kawagoe, K., Shibata, N., Morimoto, K., Higuchi, Y., Kitamura, M., Nakaya, T., Yasuoka, N.

(2000) Acta Crystallogr D Biol Crystallogr 56: 368-371

Released	2000-03-06
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	PROTEIN (FMN-BINDING PROTEIN) (protein)
Unique Ligands	FMN

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1WE5 \| pdb_00001we5	Download File View File

Crystal Structure of Alpha-Xylosidase from Escherichia coli

Ose, T., Kitamura, M., Okuyama, M., Mori, H., Kimura, A., Watanabe, N., Yao, M., Tanaka, I.

To be published

Released	2005-02-15
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Escherichia coli
Macromolecule	Putative family 31 glucosidase yicI (protein)
Unique Ligands	MES

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2CVC \| pdb_00002cvc	Download File View File

Crystal structure of High-Molecular Weight Cytochrome c from Desulfovibrio vulgaris (Hildenborough)

Suto, K., Sato, M., Shibata, N., Kitamura, M., Morimoto, Y., Takayama, Y., Ozawa, K., Akutsu, H., Higuchi, Y., Yasuoka, N.

To be published

Released	2006-06-06
Method	X-RAY DIFFRACTION 2 Å
Organisms	Nitratidesulfovibrio vulgaris
Macromolecule	High-molecular-weight cytochrome c precursor (protein)
Unique Ligands	HEC

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2D73 \| pdb_00002d73	Download File View File

Crystal Structure Analysis of SusB

Kitamura, M., Yao, M.

(2008) J Biological Chem 283: 36328-36337

Released	2007-02-27
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Bacteroides thetaiotaomicron VPI-5482
Macromolecule	alpha-glucosidase SusB (protein)
Unique Ligands	CA

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2E84 \| pdb_00002e84	Download File View File

Crystal structure of High-Molecular Weight Cytochrome c from Desulfovibrio vulgaris (Miyazaki F) in the presence of zinc ion

Shibata, N., Suto, K., Sato, M., Morimoto, Y., Kitamura, M., Higuchi, Y.

To be published

Released	2008-01-15
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	High-molecular-weight cytochrome c (protein)
Unique Ligands	HEM, NA, ZN

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2ZQ0 \| pdb_00002zq0	Download File View File

Crystal structure of SusB complexed with acarbose

Yao, M., Tanaka, I., Kitamura, M.

(2008) J Biological Chem 283: 36328-36337

Released	2008-10-28
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Bacteroides thetaiotaomicron
Macromolecule	Alpha-glucosidase (Alpha-glucosidase SusB) (protein)
Unique Ligands	CA
Unique branched monosaccharides	AC1, GLC

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3A24 \| pdb_00003a24	Download File View File

Crystal structure of BT1871 retaining glycosidase

Okuyama, M., Kitamura, M., Hondoh, H., Tanaka, I., Yao, M.

(2009) J Mol Biology 392: 1232-1241

Released	2009-10-06
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Bacteroides thetaiotaomicron
Macromolecule	alpha-galactosidase (protein)
Unique Ligands	CA, MES

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3A6Q \| pdb_00003a6q	Download File View File

E13T mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)

Nakanishi, T., Haruyama, Y., Inoue, H., Kitamura, M.

(2010) J Phys Chem B 114: 6175-6182

Released	2010-09-01
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	FMN-binding protein (protein)
Unique Ligands	CL, FMN

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3A6R \| pdb_00003a6r	Download File View File

E13Q mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)

Nakanishi, T., Haruyama, Y., Inoue, H., Kitamura, M.

(2010) J Phys Chem B 114: 6175-6182

Released	2010-09-01
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	FMN-binding protein (protein)
Unique Ligands	CL, FMN

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3AMF \| pdb_00003amf	Download File View File

E13R mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)

Sato, S., Nakanishi, T., Inoue, H., Kitamura, M.

To be published

Released	2011-10-05
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	FMN-binding protein (protein)
Unique Ligands	CL, FMN

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3AWH \| pdb_00003awh	Download File View File

E13K mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)

Sato, S., Nakanishi, T., Inoue, H., Kitamura, M.

To be published

Released	2012-04-18
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	FMN-binding protein (protein)
Unique Ligands	CL, FMN

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3VQT \| pdb_00003vqt	Download File View File

Crystal structure analysis of the translation factor RF3

Kihira, K., Shomura, Y., Shibata, N., Kitamura, M., Higuchi, Y.

(2012) FEBS Lett 586: 3705-3709

Released	2012-09-05
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	Peptide chain release factor 3 (protein)
Unique Ligands	GDP

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3VR1 \| pdb_00003vr1	Download File View File

Crystal structure analysis of the translation factor RF3

Kihira, K., Shomura, Y., Shibata, N., Kitamura, M., Higuchi, Y.

(2012) FEBS Lett 586: 3705-3709

Released	2012-09-05
Method	X-RAY DIFFRACTION 3 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	Peptide chain release factor 3 (protein)
Unique Ligands	G4P

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3VY2 \| pdb_00003vy2	Download File View File

N33D mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)

Takagi, R., Nakanishi, T., Kitamura, M.

To be published

Released	2013-09-25
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	FMN-binding protein (protein)
Unique Ligands	FMN

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3VY5 \| pdb_00003vy5	Download File View File

N33Q mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)

Takagi, R., Nakanishi, T., Kitamura, M.

To be published

Released	2013-09-25
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	FMN-binding protein (protein)
Unique Ligands	CL, FMN

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3VYA \| pdb_00003vya	Download File View File

W32Y mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)

Takagi, R., Nakanishi, T., Kitamura, M.

To be published

Released	2013-09-25
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	FMN-binding protein (protein)
Unique Ligands	FMN

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3W8Q \| pdb_00003w8q	Download File View File

Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1)

Nakae, S., Kitamura, M., Shirai, T., Tada, T.

(2021) Acta Crystallogr F Struct Biol Commun 77: 459-464

Released	2014-03-26
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	Dual specificity mitogen-activated protein kinase kinase 1 (protein)
Unique Ligands	AGS

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5B37 \| pdb_00005b37	Download File View File

Crystal structure of L-tryptophan dehydrogenase from Nostoc punctiforme

Wakamatsu, T., Sakuraba, H., Kitamura, M., Hakumai, Y., Ohnishi, K., Ashiuchi, M., Ohshima, T.

(2017) Appl Environ Microbiol 83:

Released	2016-11-23
Method	X-RAY DIFFRACTION 3.4 Å
Organisms	Nostoc punctiforme NIES-2108
Macromolecule	Tryptophan dehydrogenase (protein)

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5B3K \| pdb_00005b3k	Download File View File

C101A mutant of Flavodoxin from Pseudomonas aeruginosa

Okada, D., Nakanishi, T., Kitamura, M.

To be published

Released	2017-03-08
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Pseudomonas aeruginosa PAO1
Macromolecule	Uncharacterized protein PA3435 (protein)
Unique Ligands	SO4

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5B3L \| pdb_00005b3l	Download File View File

C101S mutant of Flavodoxin from Pseudomonas aeruginosa

Okada, D., Nakanishi, T., Kitamura, M.

To be published

Released	2017-03-08
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Pseudomonas aeruginosa PAO1
Macromolecule	Uncharacterized protein PA3435 (protein)
Unique Ligands	SO4

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7EG5 \| pdb_00007eg5	Download File View File

FMN-bound form of YviC from Lactococcus lactis subsp. lactis Il1403

Sugiura, N., Nakanishi, T., Kitamura, M.

To be published

Released	2022-04-20
Method	X-RAY DIFFRACTION 1.96 Å
Organisms	Lactococcus lactis subsp. lactis Il1403
Macromolecule	FMN-binding protein (protein)
Unique Ligands	FMN

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8ITO \| pdb_00008ito	Download File View File

Crystal structure of FeRlp from Desulfovibrio vulgaris (Hildenborough)

Nakatsuji, T., Ogata, H., Kitamura, M.

To be published

Released	2024-03-27
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	Rubredoxin (protein)
Unique Ligands	FE, PO4

1 to 22 of 22 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.

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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

1FLM | pdb_00001flm

1WE5 | pdb_00001we5

2CVC | pdb_00002cvc

2D73 | pdb_00002d73

2E84 | pdb_00002e84

2ZQ0 | pdb_00002zq0

3A24 | pdb_00003a24

3A6Q | pdb_00003a6q

3A6R | pdb_00003a6r

3AMF | pdb_00003amf

3AWH | pdb_00003awh

3VQT | pdb_00003vqt

3VR1 | pdb_00003vr1

3VY2 | pdb_00003vy2

3VY5 | pdb_00003vy5

3VYA | pdb_00003vya

3W8Q | pdb_00003w8q

5B37 | pdb_00005b37

5B3K | pdb_00005b3k

5B3L | pdb_00005b3l

7EG5 | pdb_00007eg5

8ITO | pdb_00008ito