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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"

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Search Summary

This query matches 232 Structures.

Refinements

Structure Determination Methodology

experimental (232)

Scientific Name of Source Organism

	Nitratidesulfovibrio vulgaris str. Hildenborough (118)
	Nitratidesulfovibrio vulgaris (58)
	Nitratidesulfovibrio vulgaris str. 'Miyazaki F (54)
	Homo sapiens (11)
	Casadabanvirus D3112 (1)
	Desulfomicrobium norvegicum (1)
	Desulfovibrio desulfuricans (1)
	Enterobacteria phage RB59 (1)
	Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough) (1)
	Nitratidesulfovibrio vulgaris DP4 (1)

More...

Taxonomy

	Bacteria (232)
	Eukaryota (11)
	Duplodnaviria (2)
	other sequences (1)
	unclassified bacterial viruses (1)

Experimental Method

	X-RAY DIFFRACTION (210)
	SOLUTION NMR (15)
	ELECTRON MICROSCOPY (6)
	THEORETICAL MODEL (3)
	NEUTRON DIFFRACTION (2)

Polymer Entity Type

	Protein (232)
	RNA (6)
	NA-hybrid (2)
	DNA (1)

Refinement Resolution (Å)

	0.5 - 1.0 (4)
	1.0 - 1.5 (53)
	1.5 - 2.0 (85)
	2.0 - 2.5 (48)
	2.5 - 3.0 (21)
	3.0 - 3.5 (6)
	3.5 - 4.0 (1)

Release Date

	1980 - 1984 (1)
	1985 - 1989 (1)
	1990 - 1994 (8)
	1995 - 1999 (21)
	2000 - 2004 (46)
	2005 - 2009 (45)
	2010 - 2014 (28)
	2015 - 2019 (37)
	2020 - 2024 (45)

Enzyme Classification Name

	Oxidoreductases (91)
	Hydrolases (8)
	Lyases (4)

Membrane Protein Annotation

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

Symmetry Type

	Asymmetric (169)
	Cyclic (63)
	Dihedral (16)

SCOP Classification

	Multi-domain proteins (alpha and beta) (54)
	All alpha proteins (43)
	Alpha and beta proteins (a/b) (37)
	Small proteins (20)
	All beta proteins (10)
	Alpha and beta proteins (a+b) (6)
	Artifacts (5)
	Low resolution protein structures (2)
	Coiled coil proteins (1)

AllSelected

1 to 25 of 232 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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1AXJ \| pdb_00001axj	Download File View File

FMN-BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS (MIYAZAKI F), NMR, 20 STRUCTURES

Liepinsh, E., Otting, G.

(1997) Nat Struct Biol 4: 975-979

Released	1998-01-14
Method	SOLUTION NMR
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	FMN-BINDING PROTEIN (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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1BU5 \| pdb_00001bu5	Download File View File

X-RAY CRYSTAL STRUCTURE OF THE DESULFOVIBRIO VULGARIS (HILDENBOROUGH) APOFLAVODOXIN-RIBOFLAVIN COMPLEX

Walsh, M.A., Mccarthy, A., O'Farrell, P.A., Mccardle, P., Cunningham, P.D., Mayhew, S.G., Higgins, T.M.

(1998) Eur J Biochem 258: 362-371

Released	1999-02-09
Method	X-RAY DIFFRACTION 1.83 Å
Organisms	Nitratidesulfovibrio vulgaris
Macromolecule	PROTEIN (FLAVODOXIN) (protein)
Unique Ligands	RBF, SO4

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1C53 \| pdb_00001c53	Download File View File

S-CLASS CYTOCHROMES C HAVE A VARIETY OF FOLDING PATTERNS: STRUCTURE OF CYTOCHROME C-553 FROM DESULFOVIBRIO VULGARIS DETERMINED BY THE MULTI-WAVELENGTH ANOMALOUS DISPERSION METHOD

Nakagawa, A., Higuchi, Y., Yasuoka, N., Katsube, Y., Yaga, T.

(1990) J Biochem 108: 701-703

Released	1993-10-31
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	CYTOCHROME C553 (protein)
Unique Ligands	HEM

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1C7E \| pdb_00001c7e	Download File View File

D95E HYDROQUINONE FLAVODOXIN MUTANT FROM D. VULGARIS

McCarthy, A., Walsh, M., Higgins, T., D'Arcy, D.

(2002) Biochemistry 41: 10950-10962

Released	2000-08-23
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Nitratidesulfovibrio vulgaris
Macromolecule	FLAVODOXIN (protein)
Unique Ligands	FMN

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1C7F \| pdb_00001c7f	Download File View File

D95E OXIDIZED FLAVODOXIN MUTANT FROM D. VULGARIS

McCarthy, A., Walsh, M., Higgins, T., D'Arcy, D.

(2002) Biochemistry 41: 10950-10962

Released	2000-08-23
Method	X-RAY DIFFRACTION 2 Å
Organisms	Nitratidesulfovibrio vulgaris
Macromolecule	FLAVODOXIN (protein)
Unique Ligands	FMN

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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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1DVH \| pdb_00001dvh	Download File View File

STRUCTURE AND DYNAMICS OF FERROCYTOCHROME C553 FROM DESULFOVIBRIO VULGARIS STUDIED BY NMR SPECTROSCOPY AND RESTRAINED MOLECULAR DYNAMICS

Blackledge, M.J., Medvedeva, S., Poncin, M., Guerlesquin, F., Bruschi, M., Marion, D.

(1995) J Mol Biology 245: 661-681

Released	1995-06-03
Method	SOLUTION NMR
Organisms	Nitratidesulfovibrio vulgaris
Macromolecule	CYTOCHROME C553 (protein)
Unique Ligands	HEC

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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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1E1D \| pdb_00001e1d	Download File View File

Hybrid Cluster Protein from Desulfovibrio vulgaris

Arendsen, A.F., Cooper, S.J., Bailey, S., Garner, C.D., Hagen, W.R., Lindley, P.F.

(2000) Biochemistry 39: 15044

Released	2000-06-21
Method	X-RAY DIFFRACTION 1.72 Å
Organisms	Nitratidesulfovibrio vulgaris
Macromolecule	HYDROXYLAMINE REDUCTASE (protein)
Unique Ligands	FSO, SF4

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1E2U \| pdb_00001e2u	Download File View File

Low Temperature Structure of Hybrid Cluster Protein from Desulfovibrio vulgaris to 1.6A

Cooper, S.J., Bailey, S., Hagen, W.R., Lindley, P.F.

(2000) Biochemistry 39: 15044

Released	2000-12-11
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Nitratidesulfovibrio vulgaris
Macromolecule	HYDROXYLAMINE REDUCTASE (protein)
Unique Ligands	FSO, SF4

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1E9V \| pdb_00001e9v	Download File View File

XENON BOUND IN HYDROPHOBIC CHANNEL OF HYBRID CLUSTER PROTEIN FROM DESULFOVIBRIO VULGARIS

Cooper, S.J., Bailey, S., Rizkallah, P.J., Lindley, P.F.

To be published

Released	2001-10-25
Method	X-RAY DIFFRACTION 1.79 Å
Organisms	Nitratidesulfovibrio vulgaris
Macromolecule	HYDROXYLAMINE REDUCTASE (protein)
Unique Ligands	ACY, EDO, FSO, GOL, SF4, TRS, XE

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1F4P \| pdb_00001f4p	Download File View File

Y98W FLAVODOXIN MUTANT 1.5A (D. VULGARIS)

Reynolds, R.A., Watt, W., Watenpaugh, K.D.

(2001) Acta Crystallogr D Biol Crystallogr 57: 527-535

Released	2001-04-04
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Nitratidesulfovibrio vulgaris
Macromolecule	FLAVODOXIN (protein)
Unique Ligands	FMN

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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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1FX1 \| pdb_00001fx1	Download File View File

A CRYSTALLOGRAPHIC STRUCTURAL STUDY OF THE OXIDATION STATES OF DESULFOVIBRIO VULGARIS FLAVODOXIN

Watenpaugh, K.D., Sieker, L.C., Jensen, L.H.

(1976) Flavins And Flavoproteins 405

Released	1985-01-02
Method	X-RAY DIFFRACTION 2 Å
Organisms	Nitratidesulfovibrio vulgaris
Macromolecule	FLAVODOXIN (protein)
Unique Ligands	FMN

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1GNT \| pdb_00001gnt	Download File View File

Hybrid Cluster Protein from Desulfovibrio vulgaris. X-ray structure at 1.25A resolution using synchrotron radiation.

Macedo, S., Mitchell, E.P., Romao, C.V., Cooper, S.J., Coelho, R., Liu, M.Y., Xavier, A.V., Legall, J., Bailey, S., Garner, D.C., Hagen, W.R., Teixeira, M., Carrondo, M.A., Lindley, P.

(2002) J Biol Inorg Chem 7: 514-525

Released	2002-04-11
Method	X-RAY DIFFRACTION 1.25 Å
Organisms	Nitratidesulfovibrio vulgaris
Macromolecule	HYBRID CLUSTER PROTEIN (protein)
Unique Ligands	FSO, SF4

1 to 25 of 232 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

1AXJ | pdb_00001axj

1AZL | pdb_00001azl

1B71 | pdb_00001b71

1BU5 | pdb_00001bu5

1C53 | pdb_00001c53

1C7E | pdb_00001c7e

1C7F | pdb_00001c7f

1DVB | pdb_00001dvb

1DVH | pdb_00001dvh

1DWL | pdb_00001dwl

1E08 | pdb_00001e08

1E1D | pdb_00001e1d

1E2U | pdb_00001e2u

1E9V | pdb_00001e9v

1F4P | pdb_00001f4p

1FLM | pdb_00001flm

1FX1 | pdb_00001fx1

1GNT | pdb_00001gnt