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235,183 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Source Organism Taxonomy Name (Full Lineage) = "Nitratidesulfovibrio vulgaris str. Hildenborough"

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Search Summary

This query matches 119 Structures.

Refinements

Structure Determination Methodology

experimental (119)

Scientific Name of Source Organism

	Nitratidesulfovibrio vulgaris str. Hildenborough (118)
	Homo sapiens (11)
	Casadabanvirus D3112 (1)
	Desulfomicrobium norvegicum (1)
	Desulfovibrio desulfuricans (1)
	Enterobacteria phage RB59 (1)
	Nitratidesulfovibrio vulgaris (1)
	Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough) (1)
	Pseudomonas aeruginosa phage DMS3mVir (1)
	synthetic construct (1)

Taxonomy

	Bacteria (119)
	Eukaryota (11)
	Duplodnaviria (2)
	other sequences (1)
	unclassified bacterial viruses (1)

Experimental Method

	X-RAY DIFFRACTION (102)
	SOLUTION NMR (11)
	ELECTRON MICROSCOPY (6)
	THEORETICAL MODEL (3)

Polymer Entity Type

	Protein (119)
	RNA (6)
	NA-hybrid (2)
	DNA (1)

Refinement Resolution (Å)

	0.5 - 1.0 (2)
	1.0 - 1.5 (18)
	1.5 - 2.0 (36)
	2.0 - 2.5 (30)
	2.5 - 3.0 (16)
	3.0 - 3.5 (5)
	3.5 - 4.0 (1)

Release Date

	1995 - 1999 (15)
	2000 - 2004 (8)
	2005 - 2009 (18)
	2010 - 2014 (16)
	2015 - 2019 (20)
	2020 - 2024 (42)

Enzyme Classification Name

	Oxidoreductases (50)
	Hydrolases (8)
	Lyases (4)

Membrane Protein Annotation

	PDBTM (17)
	MemProtMD (15)
	mpstruc (13)
	OPM (12)

Symmetry Type

	Asymmetric (89)
	Cyclic (28)
	Dihedral (10)

SCOP Classification

	Multi-domain proteins (alpha and beta) (25)
	All alpha proteins (17)
	Alpha and beta proteins (a/b) (18)
	Alpha and beta proteins (a+b) (5)
	Small proteins (10)
	Low resolution protein structures (2)
	Artifacts (4)

AllSelected

1 to 25 of 119 Structures

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1A2I \| pdb_00001a2i	Download File View File

SOLUTION STRUCTURE OF DESULFOVIBRIO VULGARIS (HILDENBOROUGH) FERROCYTOCHROME C3, NMR, 20 STRUCTURES

Messias, A.C., Kastrau, D.H.K., Costa, H.S., Legall, J., Turner, D.L., Santos, H., Xavier, A.V.

(1998) J Mol Biology 281: 719-739

Released	1998-07-08
Method	SOLUTION NMR
Organisms	Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	CYTOCHROME C3 (protein)
Unique Ligands	HEC

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1AKQ \| pdb_00001akq	Download File View File

D95A OXIDIZED FLAVODOXIN MUTANT FROM D. VULGARIS

Mccarthy, A., Walsh, M., Higgins, T.

(2002) Biochemistry 41: 10950-10962

Released	1998-12-02
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	FLAVODOXIN (protein)
Unique Ligands	FMN

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1AKR \| pdb_00001akr	Download File View File

G61A OXIDIZED FLAVODOXIN MUTANT

Mccarthy, A., Walsh, M., Higgins, T.

(1998) Biochemistry 37: 8405-8416

Released	1998-05-27
Method	X-RAY DIFFRACTION 1.58 Å
Organisms	Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	FLAVODOXIN (protein)
Unique Ligands	FMN

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1AKT \| pdb_00001akt	Download File View File

G61N OXIDIZED FLAVODOXIN MUTANT

Mccarthy, A., Walsh, M., Higgins, T.

(1998) Biochemistry 37: 8405-8416

Released	1998-05-27
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	FLAVODOXIN (protein)
Unique Ligands	FMN

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1AKU \| pdb_00001aku	Download File View File

D95A HYDROQUINONE FLAVODOXIN MUTANT FROM D. VULGARIS

Mccarthy, A., Walsh, M., Higgins, T.

(2002) Biochemistry 41: 10950-10962

Released	1998-12-02
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	FLAVODOXIN (protein)
Unique Ligands	FMN, SO4

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1AKV \| pdb_00001akv	Download File View File

D95A SEMIQUINONE FLAVODOXIN MUTANT FROM D. VULGARIS

Mccarthy, A., Walsh, M., Higgins, T.

(2002) Biochemistry 41: 10950-10962

Released	1998-12-02
Method	X-RAY DIFFRACTION 2 Å
Organisms	Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	FLAVODOXIN (protein)
Unique Ligands	FMN, SO4

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1AKW \| pdb_00001akw	Download File View File

G61L OXIDIZED FLAVODOXIN MUTANT

Mccarthy, A., Walsh, M., Higgins, T.

(1998) Biochemistry 37: 8405-8416

Released	1998-05-27
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	FLAVODOXIN (protein)
Unique Ligands	FMN

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1AZL \| pdb_00001azl	Download File View File

G61V FLAVODOXIN MUTANT FROM DESULFOVIBRIO VULGARIS

Walsh, M.A., Mccarthy, A., O'Farrell, P.A., Voordouw, G., Higgins, T., Mayhew, S.G.

(1998) Biochemistry 37: 8405-8416

Released	1998-05-20
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	FLAVODOXIN (protein)
Unique Ligands	FMN

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1B71 \| pdb_00001b71	Download File View File

RUBRERYTHRIN

Sieker, L.C., Holmes, M., Le Trong, I., Turley, S., Santarsiero, B.D., Liu, M.-Y., Legall, J., Stenkamp, R.E.

(1999) Nat Struct Biol 6: 308-309

Released	2000-01-26
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	PROTEIN (RUBRERYTHRIN) (protein)
Unique Ligands	FE, ZN

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1DVB \| pdb_00001dvb	Download File View File

RUBRERYTHRIN

Sieker, L.C., Holmes, M., Le Trong, I., Turley, S., Liu, M.Y., Legall, J., Stenkamp, R.E.

(2000) J Biol Inorg Chem 5: 505-513

Released	2000-11-17
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	RUBRERYTHRIN (protein)
Unique Ligands	FE, ZN

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1DWL \| pdb_00001dwl	Download File View File

The Ferredoxin-Cytochrome complex using heteronuclear NMR and docking simulation

Morelli, X., Guerlesquin, F., Czjzek, M., Palma, P.N.

(2000) Biochemistry 39: 2530

Released	1999-12-10
Method	SOLUTION NMR THEORETICAL MODEL
Organisms	Desulfomicrobium norvegicum Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	CYTOCHROME C553 (protein) FERREDOXIN I (protein)
Unique Ligands	HEC, SF4

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1E08 \| pdb_00001e08	Download File View File

Structural model of the [Fe]-Hydrogenase/cytochrome c553 complex combining NMR and soft-docking

Morelli, X., Czjzek, M., Hatchikian, C.E., Bornet, O., Fontecilla-Camps, J.C., Palma, N.P., Moura, J.J.G., Guerlesquin, F.

(2000) J Biological Chem 275: 23204

Released	2000-08-25
Method	SOLUTION NMR THEORETICAL MODEL
Organisms	Desulfovibrio desulfuricans Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	CYTOCHROME C553 (protein) [FE]-HYDROGENASE (LARGE SUBUNIT) (protein) [FE]-HYDROGENASE (SMALL SUBUNIT) (protein)
Unique Ligands	CMO, CYN, FE2, HEC, PDT, SF4, ZN

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1GWS \| pdb_00001gws	Download File View File

hexadecaheme high molecular weight cytochrome Hmc from Desulfovibrio vulgaris Hildenborough

Czjzek, M., Haser, R., Bruschi, M.

(2002) Structure 10: 1677

Released	2003-02-13
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	HIGH-MOLECULAR-WEIGHT CYTOCHROME C (protein)
Unique Ligands	HEC

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1GX7 \| pdb_00001gx7	Download File View File

Best model of the electron transfer complex between cytochrome c3 and [Fe]-hydrogenase

Elantak, L., Morelli, X., Bornet, O., Hatchikian, C., Czjzek, M., Dolla, A., Guerlesquin, F.

(2003) FEBS Lett 548: 1

Released	2003-07-31
Method	SOLUTION NMR THEORETICAL MODEL
Organisms	Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	CYTOCHROME C3 (protein) PERIPLASMIC [FE] HYDROGENASE LARGE SUBUNIT (protein) PERIPLASMIC [FE] HYDROGENASE SMALL SUBUNIT (protein)
Unique Ligands	CMO, CYN, FE2, HEC, PDT, SF4

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1H29 \| pdb_00001h29	Download File View File

Sulfate respiration in Desulfovibrio vulgaris Hildenborough: Structure of the 16-heme Cytochrome c HmcA at 2.5 A resolution and a view of its role in transmembrane electron transfer

Matias, P.M., Coelho, A.V., Valente, F.M.A., Placido, D., Legall, J., Xavier, A.V., Pereira, I.A.C., Carrondo, M.A.

(2002) J Biological Chem 277: 47907

Released	2002-10-02
Method	X-RAY DIFFRACTION 2.51 Å
Organisms	Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	HIGH-MOLECULAR-WEIGHT CYTOCHROME C (protein)
Unique Ligands	HEC

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1HFE \| pdb_00001hfe	Download File View File

1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS

Nicolet, Y., Piras, C., Legrand, P., Hatchikian, E.C., Fontecilla-Camps, J.C.

(1999) Structure 7: 13-23

Released	1999-04-20
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT)) (protein) PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT)) (protein)
Unique Ligands	CMO, CYN, CYS, FE2, PDT, SF4, ZN

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1MDV \| pdb_00001mdv	Download File View File

KEY ROLE OF PHENYLALANINE 20 IN CYTOCHROME C3: STRUCTURE, STABILITY AND FUNCTION STUDIES

Dolla, A., Arnoux, P., Protasevich, I., Lobachov, V., Brugna, M., Guidici-Orticoni, M.T., Haser, R., Czjzek, M., Makarov, A., Brushi, M.

(1999) Biochemistry 38: 33-41

Released	1999-05-04
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	CYTOCHROME C3 (protein)
Unique Ligands	HEM

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1QYB \| pdb_00001qyb	Download File View File

X-ray crystal structure of Desulfovibrio vulgaris rubrerythrin with zinc substituted into the [Fe(SCys)4] site and alternative diiron site structures

Jin, S., Kurtz, D.M., Liu, Z.J., Rose, J., Wang, B.C.

(2004) Biochemistry 43: 3204-3213

Released	2004-03-30
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	Rubrerythrin (protein)
Unique Ligands	FE, SO4, ZN

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1RB9 \| pdb_00001rb9	Download File View File

RUBREDOXIN FROM DESULFOVIBRIO VULGARIS REFINED ANISOTROPICALLY AT 0.92 ANGSTROMS RESOLUTION

Dauter, Z., Butterworth, S., Sieker, L.C., Sheldrick, G., Wilson, K.S.

To be published

Released	1999-02-16
Method	X-RAY DIFFRACTION 0.92 Å
Organisms	Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	RUBREDOXIN (protein)
Unique Ligands	FE2, SO4

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1RYT \| pdb_00001ryt	Download File View File

RUBRERYTHRIN

Demare, F., Kurtz, D.M., Nordlund, P.

(1996) Nat Struct Biol 3: 539-546

Released	1997-05-15
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	RUBRERYTHRIN (protein)
Unique Ligands	FE

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1W9M \| pdb_00001w9m	Download File View File

AS-isolated hybrid cluster protein from Desulfovibrio vulgaris X-ray structure at 1.35A resolution using iron anomalous signal

Aragao, D., Macedo, S., Mitchell, E.P., Coelho, D., Romao, C.V., Teixeira, M., Lindley, P.F.

(2008) Acta Crystallogr D Biol Crystallogr 64: 665

Released	2005-02-04
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	HYDROXYLAMINE REDUCTASE (protein)
Unique Ligands	FS2, SF4

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1XT6 \| pdb_00001xt6	Download File View File

S35C Flavodoxin Mutant in the semiquinone state

Artali, R., Marchini, N., Meneghetti, F., Cavazzini, D., Cassetta, A., Sassone, C., Bombieri, G., Rossi, G.L., Gilardi, G.

(2005) Acta Crystallogr D Biol Crystallogr 61: 481-484

Released	2004-12-21
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	Flavodoxin (protein)
Unique Ligands	FMN

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1YUX \| pdb_00001yux	Download File View File

Mixed valant state of nigerythrin

Iyer, R.B., Silaghi-Dumitrescu, R., Kurtz, D.M., Lanzilotta, W.N.

(2005) J Biol Inorg Chem 10: 407-416

Released	2005-06-21
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	Nigerythrin (protein)
Unique Ligands	FE, FE2

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1YUZ \| pdb_00001yuz	Download File View File

Partially Reduced State of Nigerythrin

Iyer, R.B., Silaghi-Dumitrescu, R., Kurtz, D.M., Lanzilotta, W.N.

(2005) J Biol Inorg Chem 10: 407-416

Released	2005-06-21
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	Nigerythrin (protein)
Unique Ligands	FE, FE2

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1YV1 \| pdb_00001yv1	Download File View File

Fully reduced state of nigerythrin (all ferrous)

Iyer, R.B., Silaghi-Dumitrescu, R., Kurtz, D.M., Lanzilotta, W.N.

(2005) J Biol Inorg Chem 10: 407-416

Released	2005-06-21
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	Nigerythrin (protein)
Unique Ligands	FE2

1 to 25 of 119 Structures

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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

Membrane Protein Annotation

Symmetry Type

SCOP Classification

1A2I | pdb_00001a2i

1AKQ | pdb_00001akq

1AKR | pdb_00001akr

1AKT | pdb_00001akt

1AKU | pdb_00001aku

1AKV | pdb_00001akv

1AKW | pdb_00001akw

1AZL | pdb_00001azl

1B71 | pdb_00001b71

1DVB | pdb_00001dvb

1DWL | pdb_00001dwl

1E08 | pdb_00001e08

1GWS | pdb_00001gws

1GX7 | pdb_00001gx7

1H29 | pdb_00001h29

1HFE | pdb_00001hfe

1MDV | pdb_00001mdv

1QYB | pdb_00001qyb

1RB9 | pdb_00001rb9

1RYT | pdb_00001ryt

1W9M | pdb_00001w9m

1XT6 | pdb_00001xt6

1YUX | pdb_00001yux

1YUZ | pdb_00001yuz

1YV1 | pdb_00001yv1