1S4I - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

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Biological Unit 5 (Jmol Viewer)

Biological Unit 6 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A SOD-LIKE PROTEIN FROM BACILLUS SUBTILIS

Authors :   L. Banci, I. Bertini, V. Calderone, F. Cramaro, R. Del Conte, A. Fanton S. Mangani, A. Quattrone, M. S. Viezzoli

Date :   16 Jan 04 (Deposition) - 26 Apr 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: B  (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: B,D  (1x)
Biol. Unit 6: A,C  (1x)

Keywords :   Sod, Cu-Zn Sod, Sod-Like, Superoxide Dismutase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Banci, I. Bertini, V. Calderone, F. Cramaro, R. Del Conte, A. Fantoni, S. Mangani, A. Quattrone, M. S. Viezzoli
A Prokaryotic Superoxide Dismutase Paralog Lacking Two Cu Ligands: From Largely Unstructured In Solution To Ordered I The Crystal.
Proc. Natl. Acad. Sci. Usa V. 102 7541 2005
PubMed-ID: 15897454 | Reference-DOI: 10.1073/PNAS.0502450102

Molecule 1 - SUPEROXIDE DISMUTASE-LIKE PROTEIN YOJM
	Chains	:	B, A, C, D
	EC Number	:	1.15.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	YOJM, BSU19400
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:		B
Biological Unit 2 (1x)	:	A
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D
Biological Unit 5 (1x)	:		B		D
Biological Unit 6 (1x)	:	A		C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 10)

No.	Name	Count	Type	Full Name
1	CL	4	Ligand/Ion	CHLORIDE ION
2	ZN	6	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 5 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 6 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS B:112 , HIS B:121 , ASP B:124 , PRO B:176 , CL B:402	BINDING SITE FOR RESIDUE ZN B 401
02	AC2	SOFTWARE	HIS B:86 , HIS B:112 , HIS B:121 , ASP B:124 , PRO B:176 , ZN B:401 , HOH B:830	BINDING SITE FOR RESIDUE CL B 402
03	AC3	SOFTWARE	HIS A:112 , HIS A:121 , ASP A:124 , CL A:502	BINDING SITE FOR RESIDUE ZN A 501
04	AC4	SOFTWARE	HIS A:86 , HIS A:112 , HIS A:121 , ASP A:124 , SER A:177 , ZN A:501	BINDING SITE FOR RESIDUE CL A 502
05	AC5	SOFTWARE	HIS C:112 , HIS C:121 , ASP C:124 , PRO C:176 , CL C:602	BINDING SITE FOR RESIDUE ZN C 601
06	AC6	SOFTWARE	HIS C:86 , PRO C:104 , HIS C:112 , HIS C:121 , ASP C:124 , SER C:177 , ZN C:601	BINDING SITE FOR RESIDUE CL C 602
07	AC7	SOFTWARE	HIS D:112 , HIS D:121 , ASP D:124 , PRO D:176 , CL D:702	BINDING SITE FOR RESIDUE ZN D 701
08	AC8	SOFTWARE	HIS D:86 , HIS D:112 , HIS D:121 , ASP D:124 , PRO D:176 , ZN D:701	BINDING SITE FOR RESIDUE CL D 702
09	AC9	SOFTWARE	HIS B:71 , ASP B:137 , HIS D:71 , ASP D:137	BINDING SITE FOR RESIDUE ZN B 801
10	BC1	SOFTWARE	HIS A:71 , ASP A:137 , HIS C:71 , ASP C:137	BINDING SITE FOR RESIDUE ZN A 802

Asymmetric Unit

No.	Residues
1	A:93	-	A:186
2	B:93	-	B:186
3	C:93	-	C:186
4	D:93	-	D:186

Asymmetric Unit

No.	Residues
1	Asp B:64	-	Asp B:65
2	Asp B:65	-	Glu B:66
3	Arg B:95	-	Pro B:96
4	Ser B:100	-	Ala B:101
5	Ala B:101	-	Gly B:102
6	Asn B:175	-	Pro B:176
7	Asp A:64	-	Asp A:65
8	Asp A:65	-	Glu A:66
9	Arg A:95	-	Pro A:96
10	Ala A:101	-	Gly A:102
11	Asn A:175	-	Pro A:176
12	Asp C:64	-	Asp C:65
13	Asp C:65	-	Glu C:66
14	Arg C:95	-	Pro C:96
15	Ser C:100	-	Ala C:101
16	Ala C:101	-	Gly C:102
17	Asn C:175	-	Pro C:176
18	Asp D:65	-	Glu D:66
19	Ser D:100	-	Ala D:101
20	Asn D:175	-	Pro D:176

(no "SAP(SNP)/Variant" information available for 1S4I)

(no "PROSITE Motif" information available for 1S4I)

(no "Exon" information available for 1S4I)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:151
 aligned with YOJM_BACSU | O31851 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:151
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189 
           YOJM_BACSU    40 AFGHHVQLVNREGKAVGFIEIKESDDEGLDIHISANSLRPGASLGFHIYEKGSCVRPDFESAGGPFNPLNKEHGFNNPMGHHAGDLPNLEVGADGKVDVIMNAPDTSLKKGSKLNILDEDGSAFIIHEQADDYLTNPSGNSGARIVCGALL 190
               SCOP domains d1s4ia_ A: automated matches                                                                                                                            SCOP domains
               CATH domains 1s4iA00 A:40-190  [code=2.60.40.200, no name defined]                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.....eeeeeeeee.....eeeeeee.......eeeeeee...................................eeeeee......eeeeeee..................eeeeee................eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s4i A  40 AFGHHVQLVNREGKAVGFIEIKESDDEGLDIHISANSLRPGASLGFHIYEKGSCVRPDFESAGGPFNPLNKEHGFNNPMGHHAGDLPNLEVGADGKVDVIMNAPDTSLKKGSKLNILDEDGSAFIIHEQADDYLTNPSGNSGARIVCGALL 190
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189

Chain B from PDB  Type:PROTEIN  Length:152
 aligned with YOJM_BACSU | O31851 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:152
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189  
           YOJM_BACSU    40 AFGHHVQLVNREGKAVGFIEIKESDDEGLDIHISANSLRPGASLGFHIYEKGSCVRPDFESAGGPFNPLNKEHGFNNPMGHHAGDLPNLEVGADGKVDVIMNAPDTSLKKGSKLNILDEDGSAFIIHEQADDYLTNPSGNSGARIVCGALLG 191
               SCOP domains d1s4ib_ B: automated matches                                                                                                                             SCOP domains
               CATH domains 1s4iB00 B:40-191  [code=2.60.40.200, no name defined]                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....eeeeeeeee.....eeeeeee.......eeeeeee...................................eeeeee......eeeeeee..................eeeeee................eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s4i B  40 AFGHHVQLVNREGKAVGFIEIKESDDEGLDIHISANSLRPGASLGFHIYEKGSCVRPDFESAGGPFNPLNKEHGFNNPMGHHAGDLPNLEVGADGKVDVIMNAPDTSLKKGSKLNILDEDGSAFIIHEQADDYLTNPSGNSGARIVCGALLG 191
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189

Chain C from PDB  Type:PROTEIN  Length:151
 aligned with YOJM_BACSU | O31851 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:151
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189 
           YOJM_BACSU    40 AFGHHVQLVNREGKAVGFIEIKESDDEGLDIHISANSLRPGASLGFHIYEKGSCVRPDFESAGGPFNPLNKEHGFNNPMGHHAGDLPNLEVGADGKVDVIMNAPDTSLKKGSKLNILDEDGSAFIIHEQADDYLTNPSGNSGARIVCGALL 190
               SCOP domains d1s4ic_ C: automated matches                                                                                                                            SCOP domains
               CATH domains 1s4iC00 C:40-190  [code=2.60.40.200, no name defined]                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.....eeeeeeeee.....eeeeeee.......eeeeeee...................................eeeeee......eeeeeee..................eeeeee................eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s4i C  40 AFGHHVQLVNREGKAVGFIEIKESDDEGLDIHISANSLRPGASLGFHIYEKGSCVRPDFESAGGPFNPLNKEHGFNNPMGHHAGDLPNLEVGADGKVDVIMNAPDTSLKKGSKLNILDEDGSAFIIHEQADDYLTNPSGNSGARIVCGALL 190
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189

Chain D from PDB  Type:PROTEIN  Length:151
 aligned with YOJM_BACSU | O31851 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:151
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189 
           YOJM_BACSU    40 AFGHHVQLVNREGKAVGFIEIKESDDEGLDIHISANSLRPGASLGFHIYEKGSCVRPDFESAGGPFNPLNKEHGFNNPMGHHAGDLPNLEVGADGKVDVIMNAPDTSLKKGSKLNILDEDGSAFIIHEQADDYLTNPSGNSGARIVCGALL 190
               SCOP domains d1s4id_ D: automated matches                                                                                                                            SCOP domains
               CATH domains 1s4iD00 D:40-190  [code=2.60.40.200, no name defined]                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....eeeeeeeee.....eeeeeee.......ee.eeee.......................................ee......eeeeeee..................eeeeee................eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s4i D  40 AFGHHVQLVNREGKAVGFIEIKESDDEGLDIHISANSLRPGASLGFHIYEKGSCVRPDFESAGGPFNPLNKEHGFNNPMGHHAGDLPNLEVGADGKVDVIMNAPDTSLKKGSKLNILDEDGSAFIIHEQADDYLTNPSGNSGARIVCGALL 190
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189

Legend:		→ Mismatch	(orange background)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Cu,Zn superoxide dismutase-like (165)

Family: automated matches (7)

Protein domain: automated matches (7)

Bacillus subtilis [TaxId: 1423] (4)

1a	d1s4ia_	A:
1b	d1s4ib_	B:
1c	d1s4ic_	C:
1d	d1s4id_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: [code=2.60.40.200, no name defined] (125)

Bacillus subtilis. Organism_taxid: 1423. (1)

1a	1s4iA00	A:40-190
1b	1s4iC00	C:40-190
1c	1s4iD00	D:40-190
1d	1s4iB00	B:40-191

(no "Pfam Domain" information available for 1S4I)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (YOJM_BACSU | O31851)

molecular function
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004784	superoxide dismutase activity	Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + hydrogen peroxide.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0019430	removal of superoxide radicals	Any process, acting at the cellular level, involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2).
	GO:0006801	superoxide metabolic process	The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species.
cellular component
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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	Cis Peptide Bonds
		Ala A:101 - Gly A:102	[ RasMol ]
		Ala B:101 - Gly B:102	[ RasMol ]
		Ala C:101 - Gly C:102	[ RasMol ]
		Arg A:95 - Pro A:96	[ RasMol ]
		Arg B:95 - Pro B:96	[ RasMol ]
		Arg C:95 - Pro C:96	[ RasMol ]
		Asn A:175 - Pro A:176	[ RasMol ]
		Asn B:175 - Pro B:176	[ RasMol ]
		Asn C:175 - Pro C:176	[ RasMol ]
		Asn D:175 - Pro D:176	[ RasMol ]
		Asp A:64 - Asp A:65	[ RasMol ]
		Asp A:65 - Glu A:66	[ RasMol ]
		Asp B:64 - Asp B:65	[ RasMol ]
		Asp B:65 - Glu B:66	[ RasMol ]
		Asp C:64 - Asp C:65	[ RasMol ]
		Asp C:65 - Glu C:66	[ RasMol ]
		Asp D:65 - Glu D:66	[ RasMol ]
		Ser B:100 - Ala B:101	[ RasMol ]
		Ser C:100 - Ala C:101	[ RasMol ]
		Ser D:100 - Ala D:101	[ RasMol ]

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		Biological Unit 6	[ Jena3D ]

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	1s4i
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	YOJM_BACSU \| O31851
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	1.15.1.1
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	YOJM_BACSU \| O31851
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	YOJM_BACSU \| O31851	:	1u3n 1xtl 1xtm

(no "Related Entries Specified in the PDB File" available for 1S4I)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 10)

Sites (10, 10)

SS Bonds (4, 4)

Cis Peptide Bonds (20, 20)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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