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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "van den Berg, B."

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Search Summary

This query matches 134 Structures.

Refinements

Structure Determination Methodology

experimental (134)

Scientific Name of Source Organism

	Nitratidesulfovibrio vulgaris str. Hildenborough (35)
	Acidithiobacillus ferrooxidans ATCC 23270 (13)
	Thermotoga maritima MSB8 (9)
	Escherichia coli K-12 (8)
	Desulfomicrobium baculatum (7)
	Homo sapiens (7)
	Desulfomicrobium baculatum DSM 4028 (6)
	Carboxydothermus hydrogenoformans Z-2901 (5)
	Azotobacter vinelandii (4)
	Severe acute respiratory syndrome coronavirus 2 (4)

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Taxonomy

	Bacteria (111)
	Eukaryota (12)
	Archaea (7)
	Riboviria (4)

Experimental Method

	X-RAY DIFFRACTION (132)
	ELECTRON MICROSCOPY (2)

Polymer Entity Type

Protein (134)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (27)
	1.5 - 2.0 (60)
	2.0 - 2.5 (35)
	2.5 - 3.0 (7)
	3.0 - 3.5 (4)

Release Date

	1990 - 1994 (1)
	1995 - 1999 (3)
	2000 - 2004 (1)
	2005 - 2009 (7)
	2010 - 2014 (44)
	2015 - 2019 (22)
	2020 - 2024 (56)

Enzyme Classification Name

	Oxidoreductases (110)
	Lyases (7)
	Hydrolases (10)
	Transferases (2)

Membrane Protein Annotation

	mpstruc (3)
	OPM (1)

Symmetry Type

	Asymmetric (83)
	Cyclic (41)
	Dihedral (14)

SCOP Classification

	Multi-domain proteins (alpha and beta) (38)
	Alpha and beta proteins (a/b) (14)
	Alpha and beta proteins (a+b) (5)
	All alpha proteins (3)
	All beta proteins (3)
	Artifacts (1)

AllSelected

1 to 25 of 134 Structures

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1CAO \| pdb_00001cao	Download File View File

CRYSTALLOGRAPHIC STUDIES OF THE BINDING OF PROTONATED AND UNPROTONATED INHIBITORS TO CARBONIC ANHYDRASE USING HYDROGEN SULPHIDE AND NITRATE ANIONS

Mangani, S., Hakansson, K.

(1992) Eur J Biochem 210: 867-871

Released	1994-01-31
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	CARBONIC ANHYDRASE II (protein)
Unique Ligands	H2S, ZN

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1CC1 \| pdb_00001cc1	Download File View File

CRYSTAL STRUCTURE OF A REDUCED, ACTIVE FORM OF THE NI-FE-SE HYDROGENASE FROM DESULFOMICROBIUM BACULATUM

Garcin, E., Vernede, X., Hatchikian, E.C., Volbeda, A., Frey, M., Fontecilla-Camps, J.C.

(1999) Structure 7: 557-566

Released	1999-06-01
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Desulfomicrobium baculatum
Macromolecule	HYDROGENASE (LARGE SUBUNIT) (protein) HYDROGENASE (SMALL SUBUNIT) (protein)
Unique Ligands	FCO, FE2, H2S, NI, SF4

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1CRM \| pdb_00001crm	Download File View File

STRUCTURE AND FUNCTION OF CARBONIC ANHYDRASES

Yadava, V.S., Kannan, K.K.

(1981) Biomolecular Structure, Conformation, Function And Evolution 1: 165

Released	1995-02-07
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	CARBONIC ANHYDRASE I (protein)
Unique Ligands	CL, H2S, HG

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1E3D \| pdb_00001e3d	Download File View File

[NiFe] Hydrogenase from Desulfovibrio desulfuricans ATCC 27774

Matias, P.M., Soares, C.M., Saraiva, L.M., Coelho, R., Morais, J., Le Gall, J., Carrondo, M.A.

(2001) J Biol Inorg Chem 6: 63-81

Released	2001-06-14
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Desulfovibrio desulfuricans
Macromolecule	[NiFe] hydrogenase large subunit (protein) [NiFe] hydrogenase small subunit (protein)
Unique Ligands	F3S, FNE, FSX, H2S, MG, SF4

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1MOH \| pdb_00001moh	Download File View File

FERRIC MONOMERIC HEMOGLOBIN I (HB I)

Rizzi, M., Wittenberg, J.B., Ascenzi, P., Bolognesi, M.

(1996) J Mol Biology 258: 1-5

Released	1996-08-01
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Phacoides pectinatus
Macromolecule	MONOMERIC HEMOGLOBIN I (protein)
Unique Ligands	H2S, HEM

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1VCK \| pdb_00001vck	Download File View File

Crystal structure of ferredoxin component of carbazole 1,9a-dioxygenase of Pseudomonas resinovorans strain CA10

Nam, J.-W., Noguchi, H., Fujiomoto, Z., Mizuno, H., Fushinobu, S., Kobashi, N., Iwata, K., Yoshida, T., Habe, H., Yamane, H., Omori, T., Nojiri, H.

(2005) Proteins 58: 779-789

Released	2005-03-01
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Metapseudomonas resinovorans
Macromolecule	ferredoxin component of carbazole (protein)
Unique Ligands	FE, FES, H2S

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1YQ9 \| pdb_00001yq9	Download File View File

Structure of the unready oxidized form of [NiFe] hydrogenase

Volbeda, A., Martin, L., Cavazza, C., Matho, M., Faber, B.W., Roseboom, W., Albracht, S.P., Garcin, E., Rousset, M., Fontecilla-Camps, J.C.

(2005) J Biol Inorg Chem 10: 239-249

Released	2005-04-19
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Megalodesulfovibrio gigas
Macromolecule	Periplasmic [NiFe] hydrogenase large subunit (protein) Periplasmic [NiFe] hydrogenase small subunit (protein)
Unique Ligands	F3S, FCO, GOL, H2S, MG, NI, PER, SF4

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3GIT \| pdb_00003git	Download File View File

Crystal structure of a truncated acetyl-CoA synthase

Volbeda, A., Darnault, C., Fontecilla-Camps, J.C.

(2009) Biochemistry 48: 7916-7926

Released	2009-10-06
Method	X-RAY DIFFRACTION 3 Å
Organisms	Moorella thermoacetica
Macromolecule	Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha (protein)
Unique Ligands	GOL, H2S, SF4, SO4, ZN

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3HYV \| pdb_00003hyv	Download File View File

3-D X-Ray structure of the sulfide:quinone oxidoreductase from the hyperthermophilic bacterium Aquifex aeolicus

Marcia, M., Ermler, U., Peng, G.H., Michel, H.

(2009) Proc Natl Acad Sci U S A 106: 9625-9630

Released	2009-07-14
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Aquifex aeolicus
Macromolecule	Sulfide-quinone reductase (protein)
Unique Ligands	FAD, H2S, LMT, MES, PS9, SO4

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3HYW \| pdb_00003hyw	Download File View File

3-D X-Ray structure of the sulfide:quinone oxidoreductase of the hyperthermophilic bacterium Aquifex aeolicus in complex with decylubiquinone

Marcia, M., Ermler, U., Peng, G.H., Michel, H.

(2009) Proc Natl Acad Sci U S A 106: 9625-9630

Released	2009-07-14
Method	X-RAY DIFFRACTION 2 Å
Organisms	Aquifex aeolicus
Macromolecule	Sulfide-quinone reductase (protein)
Unique Ligands	DCQ, FAD, H2S, LMT, PS9, SO4

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3HYX \| pdb_00003hyx	Download File View File

3-D X-Ray structure of the sulfide:quinone oxidoreductase from Aquifex aeolicus in complex with Aurachin C

Marcia, M., Ermler, U., Peng, G.H., Michel, H.

(2009) Proc Natl Acad Sci U S A 106: 9625-9630

Released	2009-07-14
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Aquifex aeolicus
Macromolecule	Sulfide-quinone reductase (protein)
Unique Ligands	AUK, FAD, H2S, LMT, PS9, SO4

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3IIZ \| pdb_00003iiz	Download File View File

X-ray structure of the FeFe-hydrogenase maturase HydE from T. maritima in complex with S-adenosyl-L-methionine

Nicolet, Y., Amara, P., Mouesca, J.M., Fontecilla-Camps, J.C.

(2009) Proc Natl Acad Sci U S A

Released	2009-09-22
Method	X-RAY DIFFRACTION 1.62 Å
Organisms	Thermotoga maritima
Macromolecule	Biotin synthetase, putative (protein)
Unique Ligands	CL, CO3, CPS, FES, H2S, SAM, SF4

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3KPK \| pdb_00003kpk	Download File View File

Crystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans, C160A mutant

Cherney, M.M., Zhang, Y., Solomonson, M., Weiner, J.H., James, M.N.G.

(2010) J Mol Biology 398: 292-305

Released	2010-04-07
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Acidithiobacillus ferrooxidans ATCC 23270
Macromolecule	Sulfide-quinone reductase, putative (protein)
Unique Ligands	FAD, H2S, LMT, PGR

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3MMB \| pdb_00003mmb	Download File View File

Dissimilatory sulfite reductase in complex with the endproduct sulfide

Parey, K., Warkentin, E., Kroneck, P.M.H., Ermler, U.

(2010) Biochemistry 49: 8912-8921

Released	2010-07-21
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	Sulfite reductase, dissimilatory-type subunit alpha (protein) Sulfite reductase, dissimilatory-type subunit beta (protein)
Unique Ligands	H2S, SF4, SRM

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3O3M \| pdb_00003o3m	Download File View File

(R)-2-Hydroxyisocaproyl-CoA Dehydratase

Knauer, S.H., Buckel, W., Dobbek, H.

(2011) J Am Chem Soc 133: 4342-4347

Released	2011-03-16
Method	X-RAY DIFFRACTION 1.82 Å
Organisms	Clostridioides difficile
Macromolecule	alpha subunit 2-hydroxyisocaproyl-CoA dehydratase (protein) beta subunit 2-hydroxyacyl-CoA dehydratase (protein)
Unique Ligands	H2S, SF4, SO4

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3O3N \| pdb_00003o3n	Download File View File

(R)-2-hydroxyisocaproyl-CoA dehydratase in complex with its substrate (R)-2-hydroxyisocaproyl-CoA

Knauer, S.H., Buckel, W., Dobbek, H.

(2011) J Am Chem Soc 133: 4342-4347

Released	2011-03-16
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Clostridioides difficile
Macromolecule	alpha-subunit 2-hydroxyisocaproyl-CoA dehydratase (protein) beta-subunit 2-hydroxyacyl-CoA dehydratase (protein)
Unique Ligands	H2S, IRC, SF4

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3O3O \| pdb_00003o3o	Download File View File

(R)-2-hydroxyisocaproyl-CoA dehydratase in complex with (R)-2-hydroxyisocaproate

Knauer, S.H., Buckel, W., Dobbek, H.

(2011) J Am Chem Soc 133: 4342-4347

Released	2011-03-16
Method	X-RAY DIFFRACTION 2 Å
Organisms	Clostridioides difficile
Macromolecule	alpha-subunit 2-hydroxyisocaproyl-CoA dehydratase (protein) beta-subunit 2-hydroxyacyl-CoA dehydratase (protein)
Unique Ligands	2RH, H2S, SF4