1XTL - JenaLib

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Biological Unit 5 (Jmol Viewer)

Biological Unit 6 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF P104H MUTANT OF SOD-LIKE PROTEIN FROM BACILLUS SUBTILIS.

Authors :   V. Calderone, S. Mangani, L. Banci, M. Benvenuti, I. Bertini, M. S. Viez A. Fantoni

Date :   22 Oct 04 (Deposition) - 04 Oct 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Sod, Cu-Zn Sod, Sod-Like, Superoxide Dismutase Mutants, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Banci, M. Benvenuti, I. Bertini, D. E. Cabelli, V. Calderone, A. Fantoni, S. Mangani, M. Migliardi, M. S. Viezzoli
From An Inactive Prokaryotic Sod Homologue To An Active Protein Through Site-Directed Mutagenesis.
J. Am. Chem. Soc. V. 127 13287 2005
PubMed-ID: 16173759 | Reference-DOI: 10.1021/JA052790O
(for further references see the PDB file header)

Molecule 1 - HYPOTHETICAL SUPEROXIDE DISMUTASE-LIKE PROTEIN YOJM
	Chains	:	B, A, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	TOP1
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 14)

No.	Name	Count	Type	Full Name
1	CU	4	Ligand/Ion	COPPER (II) ION
2	ZN	10	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 5 (0, 0)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 6 (0, 0)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS B:86 , TYR B:88 , HIS B:104 , HIS B:166	BINDING SITE FOR RESIDUE CU B 1171
02	AC2	SOFTWARE	HIS B:104 , HIS B:112 , HIS B:121 , ASP B:124	BINDING SITE FOR RESIDUE ZN B 1172
03	AC3	SOFTWARE	HIS A:86 , TYR A:88 , HIS A:104 , HIS A:166	BINDING SITE FOR RESIDUE CU A 1173
04	AC4	SOFTWARE	HIS A:104 , HIS A:112 , HIS A:121 , ASP A:124	BINDING SITE FOR RESIDUE ZN A 1174
05	AC5	SOFTWARE	HIS C:86 , TYR C:88 , HIS C:104 , HIS C:166	BINDING SITE FOR RESIDUE CU C 1175
06	AC6	SOFTWARE	HIS C:104 , HIS C:112 , HIS C:121 , ASP C:124 , PRO C:176	BINDING SITE FOR RESIDUE ZN C 1176
07	AC7	SOFTWARE	HIS D:86 , TYR D:88 , HIS D:104 , HIS D:166	BINDING SITE FOR RESIDUE CU D 1177
08	AC8	SOFTWARE	HIS D:104 , HIS D:112 , HIS D:121 , ASP D:124 , PRO D:176	BINDING SITE FOR RESIDUE ZN D 1178
09	AC9	SOFTWARE	HIS B:71 , ASP B:137 , HIS C:71 , ASP C:137	BINDING SITE FOR RESIDUE ZN B 1326
10	BC1	SOFTWARE	HIS A:71 , ASP A:137 , HIS D:71 , ASP D:137	BINDING SITE FOR RESIDUE ZN A 1327
11	BC2	SOFTWARE	GLU C:89 , ASP C:157 , ASP C:159 , GLY C:160	BINDING SITE FOR RESIDUE ZN C 1328
12	BC3	SOFTWARE	GLU B:89 , ASP B:157 , ASP B:159 , GLY B:160 , HOH B:1378 , HOH B:1396	BINDING SITE FOR RESIDUE ZN B 1329
13	BC4	SOFTWARE	GLU D:89 , ASP D:157 , ASP D:159 , GLY D:160 , HOH D:1392	BINDING SITE FOR RESIDUE ZN D 1330
14	BC5	SOFTWARE	GLU A:89 , ASP A:157 , ASP A:159 , GLY A:160	BINDING SITE FOR RESIDUE ZN A 1331

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	Asn B:175	-	Pro B:176
6	Arg A:95	-	Pro A:96
7	Ser A:100	-	Ala A:101
8	Ala A:101	-	Gly A:102
9	Gly A:119	-	His A:120
10	Asn A:175	-	Pro A:176
11	Asp C:65	-	Glu C:66
12	Arg C:95	-	Pro C:96
13	Ser C:100	-	Ala C:101
14	Gly C:119	-	His C:120
15	Asn C:175	-	Pro C:176
16	Asp D:64	-	Asp D:65
17	Asp D:65	-	Glu D:66
18	Arg D:95	-	Pro D:96
19	Ser D:100	-	Ala D:101
20	Asn D:175	-	Pro D:176

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

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

(no "Exon" information available for 1XTL)

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: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 d1xtla_ A: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 1xtl A  40 AFGHHVQLVNREGKAVGFIEIKESDDEGLDIHISANSLRPGASLGFHIYEKGSCVRPDFESAGGHFNPLNKEHGFNNPMGHHAGDLPNLEVGADGKVDVIMNAPDTSLKKGSKLNILDEDGSAFIIHEQADDYLTNPSGNSGARIVCGALLG 191
                                    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 d1xtlb_ B: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 1xtl B  40 AFGHHVQLVNREGKAVGFIEIKESDDEGLDIHISANSLRPGASLGFHIYEKGSCVRPDFESAGGHFNPLNKEHGFNNPMGHHAGDLPNLEVGADGKVDVIMNAPDTSLKKGSKLNILDEDGSAFIIHEQADDYLTNPSGNSGARIVCGALLG 191
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189

Chain C 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 d1xtlc_ C: automated matches                                                                                                                             SCOP domains
               CATH domains 1xtlC00 C:40-191  [code=2.60.40.200, no name defined]                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....eeeeeeeee.....eeeeeee.......ee.eeee.......................................ee......eeeeeee..................eeeeee................eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xtl C  40 AFGHHVQLVNREGKAVGFIEIKESDDEGLDIHISANSLRPGASLGFHIYEKGSCVRPDFESAGGHFNPLNKEHGFNNPMGHHAGDLPNLEVGADGKVDVIMNAPDTSLKKGSKLNILDEDGSAFIIHEQADDYLTNPSGNSGARIVCGALLG 191
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189

Chain D 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 d1xtld_ D: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....eeeeeeee......eeeeeee.......ee.eeee.......................................ee......eeeeeee..................eeeeee................eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xtl D  40 AFGHHVQLVNREGKAVGFIEIKESDDEGLDIHISANSLRPGASLGFHIYEKGSCVRPDFESAGGHFNPLNKEHGFNNPMGHHAGDLPNLEVGADGKVDVIMNAPDTSLKKGSKLNILDEDGSAFIIHEQADDYLTNPSGNSGARIVCGALLG 191
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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	d1xtla_	A:
1b	d1xtlb_	B:
1c	d1xtlc_	C:
1d	d1xtld_	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)

1xtlC00

C:40-191

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

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
		CU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:101 - Gly A:102	[ RasMol ]
		Arg A:95 - Pro A:96	[ RasMol ]
		Arg B:95 - Pro B:96	[ RasMol ]
		Arg C:95 - Pro C:96	[ RasMol ]
		Arg D:95 - Pro D: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 B:64 - Asp B:65	[ RasMol ]
		Asp B:65 - Glu B:66	[ RasMol ]
		Asp C:65 - Glu C:66	[ RasMol ]
		Asp D:64 - Asp D:65	[ RasMol ]
		Asp D:65 - Glu D:66	[ RasMol ]
		Gly A:119 - His A:120	[ RasMol ]
		Gly C:119 - His C:120	[ RasMol ]
		Ser A:100 - Ala A:101	[ 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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	1xtl
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	YOJM_BACSU \| O31851	:	1s4i 1u3n 1xtm

1s4i	CRYSTAL STRUCTURE OF A SOD-LIKE PROTEIN FROM BACILLUS SUBTILIS CRYSTALLISED IN THE PRESENCE OF ZINC
1xtm	Y88H, P104H MUTANTS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 14)

Sites (14, 14)

SS Bonds (4, 4)

Cis Peptide Bonds (20, 20)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 4)

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Gene Ontology (10, 10)

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