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232,418 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Shimizu, K."

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Search Summary

This query matches 19 Structures.

Refinements

Structure Determination Methodology

experimental (19)

Scientific Name of Source Organism

	Pyrococcus horikoshii (6)
	Homo sapiens (3)
	Aquifex aeolicus (2)
	Bacillus sp. 41M-1 (2)
	Escherichia coli (2)
	Thermotoga maritima (2)
	Thermus thermophilus (1)
	Thermus thermophilus HB8 (1)

Taxonomy

	Bacteria (10)
	Archaea (6)
	Eukaryota (3)

Experimental Method

X-RAY DIFFRACTION (19)

Polymer Entity Type

Protein (19)

Refinement Resolution (Å)

	1.5 - 2.0 (8)
	2.0 - 2.5 (8)
	2.5 - 3.0 (3)

Release Date

	2005 - 2009 (17)
	2010 - 2014 (2)

Enzyme Classification Name

	Hydrolases (6)
	Transferases (6)
	Ligases (1)

Symmetry Type

	Cyclic (13)
	Asymmetric (12)
	Dihedral (1)

SCOP Classification

	Alpha and beta proteins (a+b) (4)
	Alpha and beta proteins (a/b) (7)
	Artifacts (1)
	All beta proteins (2)

AllSelected

1 to 19 of 19 Structures

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1VBR	Download File View File

Crystal structure of complex xylanase 10B from Thermotoga maritima with xylobiose

Ihsanawati, Kumasaka, T., Kaneko, T., Nakamura, S., Tanaka, N.

(2005) Proteins 61: 999-1009

Released	2005-06-28
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Thermotoga maritima
Macromolecule	endo-1,4-beta-xylanase B (protein)
Unique Ligands	ACY
Unique branched monosaccharides	XYP, XYS

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1VBU	Download File View File

Crystal structure of native xylanase 10B from Thermotoga maritima

Ihsanawati, Kumasaka, T., Kaneko, T., Nakamura, S., Tanaka, N.

(2005) Proteins 61: 999-1009

Released	2005-06-28
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Thermotoga maritima
Macromolecule	endo-1,4-beta-xylanase B (protein)
Unique Ligands	ACY, GOL, SO4

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1WNF	Download File View File

Crystal Structure of PH0066 from Pyrococcus horikoshii

Ihsanawati, Sekine, S., Murayama, K., Sugawara, M., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2005-02-02
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Pyrococcus horikoshii
Macromolecule	L-asparaginase (protein)
Unique Ligands	EDO

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1Z54	Download File View File

Crystal structure of a hypothetical protein TT1821 from Thermus thermophilus

Ihsanawati, Kaminishi, T., Murayama, K., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2005-09-17
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Thermus thermophilus HB8
Macromolecule	probable thioesterase (protein)
Unique Ligands	GOL

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1ZPW	Download File View File

Crystal structure of a hypothetical protein TT1823 from Thermus thermophilus

Ihsanawati, Murayama, K., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2005-11-18
Method	X-RAY DIFFRACTION 1.64 Å
Organisms	Thermus thermophilus
Macromolecule	hypothetical protein TT1823 (protein)

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2DBI	Download File View File

Crystal Structure of a Hypothetical Protein JW0805 from Escherichia coli

Ihsanawati, Murayama, K., Bessho, Y., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2006-06-15
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Escherichia coli
Macromolecule	Hypothetical protein ybiU (protein)

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2DBN	Download File View File

Crystal Structure of a Hypothetical Protein JW0805 at High pH from Escherichia coli

Ihsanawati, Murayama, K., Bessho, Y., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2006-06-15
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Escherichia coli
Macromolecule	Hypothetical protein ybiU (protein)
Unique Ligands	SO4

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2DCJ	Download File View File

A two-domain structure of alkaliphilic XynJ from Bacillus sp. 41M-1

Ihsanawati, Tanaka, N., Nakamura, S., Kumasaka, T.

To be published

Released	2007-03-20
Method	X-RAY DIFFRACTION 2.24 Å
Organisms	Bacillus sp. 41M-1
Macromolecule	xylanase J (protein)
Unique Ligands	CA, GOL, MPD

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2DCK	Download File View File

A tetragonal-lattice structure of alkaliphilic XynJ from Bacillus sp. 41M-1

Fibriansah, G., Ihsanawati, Tanaka, N., Nakamura, S., Kumasaka, T.

To be published

Released	2007-03-20
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Bacillus sp. 41M-1
Macromolecule	xylanase J (protein)
Unique Ligands	CA, GOL

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2DUL	Download File View File

Crystal structure of tRNA G26 methyltransferase Trm1 in apo form from Pyrococcus horikoshii

Ihsanawati, Shirouzu, M., Bessho, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2008) J Mol Biol 383: 871-884

Released	2007-01-24
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Pyrococcus horikoshii
Macromolecule	N(2),N(2)-dimethylguanosine tRNA methyltransferase (protein)
Unique Ligands	GOL

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2DYY	Download File View File

Crystal structure of putative translation initiation inhibitor PH0854 from Pyrococcus horikoshii

Ihsanawati, Kishishita, S., Murayama, K., Chen, L., Liu, Z.J., Wang, B.C., Shirouzu, M., Bessho, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2007-03-19
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Pyrococcus horikoshii
Macromolecule	UPF0076 protein PH0854 (protein)

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2EJT	Download File View File

Complex structure of Trm1 from Pyrococcus horikoshii with S-adenosyl-L-Methionine

Ihsanawati, Shirouzu, M., Bessho, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2008) J Mol Biol 383: 871-884

Released	2007-09-25
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Pyrococcus horikoshii
Macromolecule	N(2),N(2)-dimethylguanosine tRNA methyltransferase (protein)
Unique Ligands	GOL, SAM

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2EJU	Download File View File

Complex structure of Trm1 from Pyrococcus horikoshii with S-adenosyl-L-Homocystein

Ihsanawati, Shirouzu, M., Bessho, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2008) J Mol Biol 383: 871-884

Released	2007-09-25
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Pyrococcus horikoshii
Macromolecule	N(2),N(2)-dimethylguanosine tRNA methyltransferase (protein)
Unique Ligands	GOL, SAH

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2EK1	Download File View File

Crystal structure of RNA-binding motif of human rna-binding protein 12

Ihsanawati, Bessho, Y., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2008-04-01
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	RNA-binding protein 12 (protein)

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2YTZ	Download File View File

Complex structure of Trm1 from Pyrococcus horikoshii with S-adenosyl-L-Homocystein in the orthorhombic crystal-lattice

Ihsanawati, Shirouzu, M., Bessho, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2008) J Mol Biol 383: 871-884

Released	2007-10-09
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Pyrococcus horikoshii
Macromolecule	N(2),N(2)-dimethylguanosine tRNA methyltransferase (protein)
Unique Ligands	SAH, SO4

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2YVI	Download File View File

Crystal structure of a death domain of human ankryn protein

Ihsanawati, Bessho, Y., Chen, L., Liu, Z.J., Wang, B.C., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2008-04-15
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	Homo sapiens
Macromolecule	Ankyrin-1 (protein)
Unique Ligands	GOL

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2YVQ	Download File View File

Crystal structure of MGS domain of carbamoyl-phosphate synthetase from homo sapiens

Xie, Y., Ihsanawati, Kishishita, S., Murayama, K., Takemoto, C., Shirozu, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2008-04-15
Method	X-RAY DIFFRACTION 1.98 Å
Organisms	Homo sapiens
Macromolecule	Carbamoyl-phosphate synthase (protein)

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3AXS	Download File View File

Complex structure of tRNA methyltransferase Trm1 from Aquifex aeolicus with sinefungin

Ihsanawati, Sengoku, T., Yokoyama, S., Bessho, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2011) J Biol Chem 286: 35236-35246

Released	2011-08-03
Method	X-RAY DIFFRACTION 2.162 Å
Organisms	Aquifex aeolicus
Macromolecule	Probable N(2),N(2)-dimethylguanosine tRNA methyltransferase Trm1 (protein)
Unique Ligands	SFG, SO4, ZN

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3AXT	Download File View File

Complex structure of tRNA methyltransferase Trm1 from Aquifex aeolicus with S-adenosyl-L-Methionine

Ihsanawati, Sengoku, T., Yokoyama, S., Bessho, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2011) J Biol Chem 286: 35236-35246

Released	2011-08-03
Method	X-RAY DIFFRACTION 2.491 Å
Organisms	Aquifex aeolicus
Macromolecule	Probable N(2),N(2)-dimethylguanosine tRNA methyltransferase Trm1 (protein)
Unique Ligands	SAM, SO4, ZN

1 to 19 of 19 Structures

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