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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Benini, S."

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Search Summary

This query matches 49 Structures.

Refinements

Structure Determination Methodology

experimental (49)

Scientific Name of Source Organism

	Sporosarcina pasteurii (15)
	Erwinia amylovora CFBP1430 (8)
	Bacillus phage SF6 (6)
	Aspergillus fumigatus Af293 (2)
	Erwinia amylovora ATCC 49946 (2)
	Erwinia tasmaniensis Et1/99 (2)
	Homo sapiens (2)
	Malus domestica (2)
	Mycobacterium tuberculosis H37Rv (2)
	Rubrivivax gelatinosus (2)

More...

Taxonomy

	Bacteria (36)
	Eukaryota (7)
	Duplodnaviria (6)
	unclassified sequences (1)

Experimental Method

X-RAY DIFFRACTION (49)

Polymer Entity Type

Protein (49)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (13)
	1.5 - 2.0 (19)
	2.0 - 2.5 (10)
	2.5 - 3.0 (4)
	3.0 - 3.5 (1)
	4.0 - 4.5 (1)

Release Date

	1995 - 1999 (3)
	2000 - 2004 (7)
	2005 - 2009 (5)
	2010 - 2014 (9)
	2015 - 2019 (14)
	2020 - 2024 (11)

Enzyme Classification Name

	Hydrolases (16)
	Transferases (6)
	Oxidoreductases (3)
	Lyases (2)

Symmetry Type

	Cyclic (30)
	Asymmetric (16)
	Dihedral (9)

SCOP Classification

	All beta proteins (16)
	Alpha and beta proteins (a/b) (11)
	Alpha and beta proteins (a+b) (14)
	All alpha proteins (4)
	Artifacts (3)
	Small proteins (1)

AllSelected

1 to 25 of 49 Structures

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1B7V \| pdb_00001b7v	Download File View File

Structure of the C-553 cytochrome from Bacillus pasteruii to 1.7 A resolution

Gonzalez, A., Benini, S., Rypniewski, W.R., Wilson, K.S., Ciurli, S.

(2000) Biochemistry 39: 13115-13126

Released	2000-03-27
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Sporosarcina pasteurii
Macromolecule	PROTEIN (CYTOCHROME C-553) (protein)
Unique Ligands	HEC

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1C75 \| pdb_00001c75	Download File View File

0.97 A "AB INITIO" CRYSTAL STRUCTURE OF CYTOCHROME C-553 FROM BACILLUS PASTEURII

Benini, S., Ciurli, S., Rypniewski, W.R., Wilson, K.S.

(2000) Biochemistry 39: 13115-13126

Released	2000-03-22
Method	X-RAY DIFFRACTION 0.97 Å
Organisms	Sporosarcina pasteurii
Macromolecule	CYTOCHROME C-553 (protein)
Unique Ligands	HEC

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1HLQ \| pdb_00001hlq	Download File View File

CRYSTAL STRUCTURE OF RHODOFERAX FERMENTANS HIGH POTENTIAL IRON-SULFUR PROTEIN REFINED TO 1.45 A

Gonzalez, A., Ciurli, S., Benini, S.

(2003) Acta Crystallogr D Biol Crystallogr 59: 1582-1588

Released	2003-06-03
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Rhodoferax fermentans
Macromolecule	HIGH-POTENTIAL IRON-SULFUR PROTEIN (protein)
Unique Ligands	SF4, SO4

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1IE7 \| pdb_00001ie7	Download File View File

PHOSPHATE INHIBITED BACILLUS PASTEURII UREASE CRYSTAL STRUCTURE

Benini, S., Rypniewski, W.R., Wilson, K.S., Ciurli, S., Mangani, S.

(2001) J Biol Inorg Chem 6: 778-790

Released	2001-04-25
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Sporosarcina pasteurii
Macromolecule	UREASE ALPHA SUBUNIT (protein) UREASE BETA SUBUNIT (protein) UREASE GAMMA SUBUNIT (protein)
Unique Ligands	NI, PO4

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1RFE \| pdb_00001rfe	Download File View File

Crystal structure of conserved hypothetical protein Rv2991 from Mycobacterium tuberculosis

Benini, S., Haouz, A., Proux, F., Betton, J.M., Alzari, P., Dodson, G.G., Wilson, K.S., TB Structural Genomics Consortium (TBSGC)

(2019) J Struct Biol

Released	2004-12-28
Method	X-RAY DIFFRACTION 2 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	hypothetical protein Rv2991 (protein)

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1S3T \| pdb_00001s3t	Download File View File

BORATE INHIBITED BACILLUS PASTEURII UREASE CRYSTAL STRUCTURE

Benini, S., Rypniewski, W.R., Wilson, K.S., Ciurli, S., Mangani, S.

(2004) J Am Chem Soc 126: 3714-3715

Released	2004-04-06
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Sporosarcina pasteurii
Macromolecule	Urease alpha subunit (protein) Urease beta subunit (protein) Urease gamma subunit (protein)
Unique Ligands	BO3, NI, SO4

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1SXV \| pdb_00001sxv	Download File View File

1.3A Crystal structure of rv3628, Mycobacterium tuberculosis inorganic pyrophosphatase (PPase) at pH5.0

Benini, S., Wilson, K.S.

To be published

Released	2005-04-12
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	Inorganic pyrophosphatase (protein)
Unique Ligands	GOL, SO4

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1UBP \| pdb_00001ubp	Download File View File

CRYSTAL STRUCTURE OF UREASE FROM BACILLUS PASTEURII INHIBITED WITH BETA-MERCAPTOETHANOL AT 1.65 ANGSTROMS RESOLUTION

Benini, S., Rypniewski, W.R., Wilson, K.S., Ciurli, S., Mangani, S.

(1998) J Biol Inorg Chem 3: 268-273

Released	1999-03-02
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Sporosarcina pasteurii
Macromolecule	UREASE (protein)
Unique Ligands	BME, NI

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1WCF \| pdb_00001wcf	Download File View File

1.54 A CRYSTAL STRUCTURE OF RV3628, MYCOBACTERIUM TUBERCULOSIS INORGANIC PYROPHOSPHATASE (PPASE) AT PH7.0

Benini, S., Wilson, K.S.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 866

Released	2006-07-12
Method	X-RAY DIFFRACTION 1.54 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	INORGANIC PYROPHOSPHATASE (protein)
Unique Ligands	K, PO4

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2CMP \| pdb_00002cmp	Download File View File

crystal structure of the DNA binding domain of G1P SMALL TERMINASE SUBUNIT from bacteriophage SF6

Benini, S., Chechik, M., Ortiz-Lombardia, M., Polier, S., Shevtsov, M.B., DeLuchi, D., Alonso, J.C., Antson, A.A.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 376

Released	2007-05-15
Method	X-RAY DIFFRACTION 1.58 Å
Organisms	Bacillus phage SF6
Macromolecule	TERMINASE SMALL SUBUNIT (protein)

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2J8W \| pdb_00002j8w	Download File View File

The crystal structure of cytochrome c' from Rubrivivax gelatinosus at 1.3 A Resolution and pH 8.0

Benini, S., Ciurli, S., Rypniewski, W.R., Wilson, K.S.

(2008) J Inorg Biochem 102: 1322-1328

Released	2007-11-06
Method	X-RAY DIFFRACTION 1.29 Å
Organisms	Rubrivivax gelatinosus
Macromolecule	CYTOCHROME C' (protein)
Unique Ligands	HEC

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2J9B \| pdb_00002j9b	Download File View File

THE CRYSTAL STRUCTURE OF CYTOCHROME C' FROM RUBRIVIVAX GELATINOSUS AT 1.5 A RESOLUTION AND PH 6.3

Benini, S., Ciurli, S., Rypniewski, W.R., Wilson, K.S.

(2008) J Inorg Biochem 102: 1322-1328

Released	2007-12-04
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Rubrivivax gelatinosus
Macromolecule	CYTOCHROME C' (protein)
Unique Ligands	HEC

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2UBP \| pdb_00002ubp	Download File View File

STRUCTURE OF NATIVE UREASE FROM BACILLUS PASTEURII

Benini, S., Rypniewski, W.R., Wilson, K.S., Ciurli, S., Mangani, S.

(1999) Structure 7: 205-216

Released	1999-11-08
Method	X-RAY DIFFRACTION 2 Å
Organisms	Sporosarcina pasteurii
Macromolecule	PROTEIN (UREASE ALPHA SUBUNIT) (protein) PROTEIN (UREASE BETA SUBUNIT) (protein) PROTEIN (UREASE GAMMA SUBUNIT) (protein)
Unique Ligands	NI, SO4

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2Y3Y \| pdb_00002y3y	Download File View File

Holo-Ni(II) HpNikR is a symmetric tetramer containing four canonic square-planar Ni(II) ions at physiological pH

Benini, S., Cianci, M., Ciurli, S.

(2011) Dalton Trans 40: 7831

Released	2011-08-17
Method	X-RAY DIFFRACTION 2.39 Å
Organisms	Helicobacter pylori G27 unidentified
Macromolecule	PUTATIVE NICKEL-RESPONSIVE REGULATOR (protein) UNDECAPEPTIDE-GSSSGSASGAG (protein)
Unique Ligands	EPE, NI, PEG

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3UBP \| pdb_00003ubp	Download File View File

DIAMIDOPHOSPHATE INHIBITED BACILLUS PASTEURII UREASE

Benini, S., Rypniewski, W.R., Wilson, K.S., Miletti, S., Mangani, S., Ciurli, S.

(1999) Structure 7: 205-216

Released	1999-12-17
Method	X-RAY DIFFRACTION 2 Å
Organisms	Sporosarcina pasteurii
Macromolecule	PROTEIN (UREASE ALPHA SUBUNIT) (protein) PROTEIN (UREASE BETA SUBUNIT) (protein) PROTEIN (UREASE GAMMA SUBUNIT) (protein)
Unique Ligands	2PA, NI

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3ZQM \| pdb_00003zqm	Download File View File

Crystal structure of the small terminase oligomerization core domain from a SPP1-like bacteriophage (crystal form 1)

Buttner, C.R., Chechik, M., Ortiz-Lombardia, M., Smits, C., Chechik, V., Jeschke, G., Dykeman, E., Benini, S., Alonso, J.C., Antson, A.A.

(2012) Proc Natl Acad Sci U S A 109: 811

Released	2011-12-28
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Bacillus phage SF6
Macromolecule	TERMINASE SMALL SUBUNIT (protein)

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3ZQN \| pdb_00003zqn	Download File View File

Crystal structure of the small terminase oligomerization core domain from a SPP1-like bacteriophage (crystal form 2)

Buttner, C.R., Chechik, M., Ortiz-Lombardia, M., Smits, C., Chechik, V., Jeschke, G., Dykeman, E., Benini, S., Alonso, J.C., Antson, A.A.

(2012) Proc Natl Acad Sci U S A 109: 811

Released	2011-12-28
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Bacillus phage SF6
Macromolecule	TERMINASE SMALL SUBUNIT (protein)

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3ZQO \| pdb_00003zqo	Download File View File

Crystal structure of the small terminase oligomerization core domain from a SPP1-like bacteriophage (crystal form 3)

Buttner, C.R., Chechik, M., Ortiz-Lombardia, M., Smits, C., Chechik, V., Jeschke, G., Dykeman, E., Benini, S., Alonso, J.C., Antson, A.A.

(2012) Proc Natl Acad Sci U S A 109: 811

Released	2011-12-28
Method	X-RAY DIFFRACTION 1.68 Å
Organisms	Bacillus phage SF6
Macromolecule	TERMINASE SMALL SUBUNIT (protein)
Unique Ligands	K

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3ZQP \| pdb_00003zqp	Download File View File

Crystal structure of the small terminase oligomerization domain from a SPP1-like bacteriophage

Buttner, C.R., Chechik, M., Ortiz-Lombardia, M., Smits, C., Chechik, V., Jeschke, G., Dykeman, E., Benini, S., Alonso, J.C., Antson, A.A.

(2012) Proc Natl Acad Sci U S A 109: 811

Released	2011-12-28
Method	X-RAY DIFFRACTION 3 Å
Organisms	Bacillus phage SF6
Macromolecule	TERMINASE SMALL SUBUNIT (protein)

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3ZQQ \| pdb_00003zqq	Download File View File

Crystal structure of the full-length small terminase from a SPP1-like bacteriophage

Buttner, C.R., Chechik, M., Ortiz-Lombardia, M., Smits, C., Chechik, V., Jeschke, G., Dykeman, E., Benini, S., Alonso, J.C., Antson, A.A.

(2012) Proc Natl Acad Sci U S A 109: 811

Released	2011-12-28
Method	X-RAY DIFFRACTION 4 Å
Organisms	Bacillus phage SF6
Macromolecule	TERMINASE SMALL SUBUNIT (protein)

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4AC7 \| pdb_00004ac7	Download File View File

The crystal structure of Sporosarcina pasteurii urease in complex with citrate

Benini, S., Kosikowska, P., Cianci, M., Gonzalez Vara, A., Berlicki, L., Ciurli, S.

(2013) J Biol Inorg Chem 18: 391

Released	2013-01-16
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Sporosarcina pasteurii
Macromolecule	UREASE SUBUNIT ALPHA (protein) UREASE SUBUNIT BETA (protein) UREASE SUBUNIT GAMMA (protein)
Unique Ligands	EDO, FLC, NI, OH, SO4

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4CEU \| pdb_00004ceu	Download File View File

1.58 A resolution native Sporosarcina pasteurii urease

Benini, S., Cianci, M., Ciurli, S.

(2014) J Biol Inorg Chem 19: 1243

Released	2014-08-27
Method	X-RAY DIFFRACTION 1.58 Å
Organisms	Sporosarcina pasteurii
Macromolecule	UREASE SUBUNIT ALPHA (protein) UREASE SUBUNIT BETA (protein) UREASE SUBUNIT GAMMA (protein)
Unique Ligands	EDO, NI, OH, SO4

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4CEX \| pdb_00004cex	Download File View File

1.59 A resolution Fluoride inhibited Sporosarcina pasteurii urease

Benini, S., Cianci, M., Ciurli, S.

(2014) J Biol Inorg Chem 19: 1243

Released	2014-08-27
Method	X-RAY DIFFRACTION 1.589 Å
Organisms	Sporosarcina pasteurii
Macromolecule	UREASE SUBUNIT ALPHA (protein) UREASE SUBUNIT BETA (protein) UREASE SUBUNIT GAMMA (protein)
Unique Ligands	EDO, F, NI, SO4