1XTM - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE DOUBLE MUTANT Y88H-P104H OF A SOD-LIKE PROTEIN FROM BACILLUS SUBTILIS.

Authors :   V. Calderone, S. Mangani, L. Banci, M. Benvenuti, I. Bertini, A. Fanton M. S. Viezzoli

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

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym. Unit : A,B
Biol. Unit 1: A (1x),B (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (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
	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
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A (1x)	B (1x)
Biological Unit 2 (1x)	:	A
Biological Unit 3 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 7)

No.	Name	Count	Type	Full Name
1	CU	2	Ligand/Ion	COPPER (II) ION
2	ZN	5	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

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS B:86 , HIS B:88 , HIS B:104 , HIS B:166 , HOH B:508	BINDING SITE FOR RESIDUE CU B 500
2	AC2	SOFTWARE	HIS B:104 , HIS B:112 , HIS B:121 , ASP B:124	BINDING SITE FOR RESIDUE ZN B 501
3	AC3	SOFTWARE	HIS A:71 , ASP A:137 , HIS B:71 , ASP B:137	BINDING SITE FOR RESIDUE ZN B 502
4	AC4	SOFTWARE	HIS A:86 , HIS A:88 , HIS A:104 , HIS A:166	BINDING SITE FOR RESIDUE CU A 503
5	AC5	SOFTWARE	HIS A:104 , HIS A:112 , HIS A:121 , ASP A:124	BINDING SITE FOR RESIDUE ZN A 504
6	AC6	SOFTWARE	HIS B:120 , ASP B:144 , HOH B:553 , HOH B:642	BINDING SITE FOR RESIDUE ZN B 505
7	AC7	SOFTWARE	GLU B:89 , ASP B:157 , ASP B:159 , GLY B:160 , HOH B:628	BINDING SITE FOR RESIDUE ZN B 506

Asymmetric Unit

No.	Residues
1	A:93	-	A:186
2	B:93	-	B: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	Gly B:119	-	His B:120
5	Asn B:175	-	Pro B:176
6	Asp A:64	-	Asp A:65
7	Asp A:65	-	Glu A:66
8	Arg A:95	-	Pro A:96
9	Ser A:100	-	Ala A:101
10	Ala A:101	-	Gly A:102
11	Gly A:102	-	Gly A:103
12	Asn A:175	-	Pro A:176

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

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

(no "Exon" information available for 1XTM)

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 d1xtma_ A: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 1xtm A  40 AFGHHVQLVNREGKAVGFIEIKESDDEGLDIHISANSLRPGASLGFHIHEKGSCVRPDFESAGGHFNPLNKEHGFNNPMGHHAGDLPNLEVGADGKVDVIMNAPDTSLKKGSKLNILDEDGSAFIIHEQADDYLTNPSGNSGARIVCGALLG 191
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189

Chain B from PDB  Type:PROTEIN  Length:153
 aligned with YOJM_BACSU | O31851 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:153
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188   
           YOJM_BACSU    39 SAFGHHVQLVNREGKAVGFIEIKESDDEGLDIHISANSLRPGASLGFHIYEKGSCVRPDFESAGGPFNPLNKEHGFNNPMGHHAGDLPNLEVGADGKVDVIMNAPDTSLKKGSKLNILDEDGSAFIIHEQADDYLTNPSGNSGARIVCGALLG 191
               SCOP domains d1xtmb_ B: automated matches                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Sod_Cu-1xtmB01 B:41-189                                                                                                                              -- Pfam domains (1)
           Pfam domains (2) --Sod_Cu-1xtmB02 B:41-189                                                                                                                              -- Pfam domains (2)
         Sec.struct. author ...eeeeeeee....eeeeeeeee.....eeeeeee.......ee.eeee.........hhhhh.........................ee......eeeeeee..................eeeeee................eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xtm B  39 SAFGHHVQLVNREGKAVGFIEIKESDDEGLDIHISANSLRPGASLGFHIHEKGSCVRPDFESAGGHFNPLNKEHGFNNPMGHHAGDLPNLEVGADGKVDVIMNAPDTSLKKGSKLNILDEDGSAFIIHEQADDYLTNPSGNSGARIVCGALLG 191
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188

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	d1xtma_	A:
1b	d1xtmb_	B:

(no "CATH Domain" information available for 1XTM)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Sod_Cu] (71)

Family: Sod_Cu (71)

Bacillus subtilis (2)

1a	Sod_Cu-1xtmB01	B:41-189
1b	Sod_Cu-1xtmB02	B:41-189

Asymmetric Unit(hide GO term definitions)

Chain A,B (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
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
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		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ 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 ]
		Asn A:175 - Pro A:176	[ RasMol ]
		Asn B:175 - Pro B: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 ]
		Gly A:102 - Gly A:103	[ RasMol ]
		Gly B:119 - His B:120	[ RasMol ]
		Ser A:100 - Ala A:101	[ RasMol ]

Biological Units
	Complete Structure
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	1xtm
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
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	YOJM_BACSU \| O31851
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	YOJM_BACSU \| O31851
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UniProtKB/Swiss-Prot
	YOJM_BACSU \| O31851	:	1s4i 1u3n 1xtl

1s4i	CRYSTAL STRUCTURE OF A SOD-LIKE PROTEIN FROM BACILLUS SUBTILIS CRYSTALLISED IN THE PRESENCE OF ZINC
1xtl	CRYSTAL STRUCTURE OF P104H MUTANT OF SOD-LIKE PROTEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

SS Bonds (2, 2)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (10, 10)

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