1DT0 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CLONING, SEQUENCE, AND CRYSTALLOGRAPHIC STRUCTURE OF RECOMBINANT IRON SUPEROXIDE DISMUTASE FROM PSEUDOMONAS OVALIS

Authors :   C. J. Bond, J. Huang, R. Hajduk, K. Flick, P. Heath, B. L. Stoddard

Date :   10 Jan 00 (Deposition) - 20 Dec 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C  (2x)

Keywords :   Superoxide Dismutase, Pseudomonas Ovalis, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. J. Bond, J. Huang, R. Hajduk, K. E. Flick, P. J. Heath, B. L. Stoddard
Cloning, Sequence And Crystallographic Structure Of Recombinant Iron Superoxide Dismutase From Pseudomonas Ovalis.
Acta Crystallogr. , Sect. D V. 56 1359 2000
PubMed-ID: 11053832 | Reference-DOI: 10.1107/S0907444900009537
(for further references see the PDB file header)

Molecule 1 - SUPEROXIDE DISMUTASE
	Chains	:	A, B, C
	EC Number	:	1.15.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Gene	:	PSEUDOMONAS OVALIS CHROMOSOMAL PLASMID LIBRARY
	Expression System Plasmid	:	PTRC99A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	303

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	FE	3	Ligand/Ion	FE (III) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:26 , HIS A:73 , ASP A:156 , HIS A:160 , HOH A:1769	BINDING SITE FOR RESIDUE FE A 1601
2	AC2	SOFTWARE	HIS B:26 , HIS B:73 , ASP B:156 , HIS B:160 , HOH B:793	BINDING SITE FOR RESIDUE FE C 1602
3	AC3	SOFTWARE	HIS C:26 , HIS C:73 , ASP C:156 , HIS C:160	BINDING SITE FOR RESIDUE FE C 1603

(no "SS Bond" information available for 1DT0)

Asymmetric Unit

No.	Residues
1	Gln A:15	-	Pro A:16
2	Gln B:15	-	Pro B:16
3	Gln C:15	-	Pro C:16

(no "SAP(SNP)/Variant" information available for 1DT0)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_MN	PS00088	Manganese and iron superoxide dismutases signature.	SODF_PSEPU	157-164	3	A:156-163 B:156-163 C:156-163

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_MN	PS00088	Manganese and iron superoxide dismutases signature.	SODF_PSEPU	157-164	2	A:156-163 B:156-163 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_MN	PS00088	Manganese and iron superoxide dismutases signature.	SODF_PSEPU	157-164	2	- - C:156-163

(no "Exon" information available for 1DT0)

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:197
 aligned with SODF_PSEPU | P09223 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:197
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       
           SODF_PSEPU     2 AFELPPLPYAHDALQPHISKETLEFHHDKHHNTYVVNLNNLVPGTEFEGKTLEEIVKTSSGGIFNNAAQVWNHTFYWNCLAPNAGGQPTGALADAINAAFGSFDKFKEEFTKTSVGTFGSGWGWLVKKADGSLALASTIGAGCPLTSGDTPLLTCDVWEHAYYIDYRNLRPKYVEAFWNLVNWAFVAEQFEGKTFKA 198
               SCOP domains d1dt0a1 A:1-83 Fe superoxide dismutase (FeSOD)                                     d1dt0a2 A:84-197 Fe superoxide dismutase (FeSOD)                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee...hhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ---------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dt0 A   1 AFELPPLPYAHDALQPHISKETLEFHHDKHHNTYVVNLNNLVPGTEFEGKTLEEIVKTSSGGIFNNAAQVWNHTFYWNCLSPNAGGQPTGALADAINAAFGSFDKFKEEFTKTSVGTFGSGWGWLVKKADGSLALASTIGAGCPLTIGDTPLLTCDVWEHAYYIDYRNLRPKYVEAFWNLVNWAFVAEQFEGKTYKV 197
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain B from PDB  Type:PROTEIN  Length:197
 aligned with SODF_PSEPU | P09223 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:197
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       
           SODF_PSEPU     2 AFELPPLPYAHDALQPHISKETLEFHHDKHHNTYVVNLNNLVPGTEFEGKTLEEIVKTSSGGIFNNAAQVWNHTFYWNCLAPNAGGQPTGALADAINAAFGSFDKFKEEFTKTSVGTFGSGWGWLVKKADGSLALASTIGAGCPLTSGDTPLLTCDVWEHAYYIDYRNLRPKYVEAFWNLVNWAFVAEQFEGKTFKA 198
               SCOP domains d1dt0b1 B:1-83 Fe superoxide dismutase (FeSOD)                                     d1dt0b2 B:84-197 Fe superoxide dismutase (FeSOD)                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee...hhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ---------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dt0 B   1 AFELPPLPYAHDALQPHISKETLEFHHDKHHNTYVVNLNNLVPGTEFEGKTLEEIVKTSSGGIFNNAAQVWNHTFYWNCLSPNAGGQPTGALADAINAAFGSFDKFKEEFTKTSVGTFGSGWGWLVKKADGSLALASTIGAGCPLTIGDTPLLTCDVWEHAYYIDYRNLRPKYVEAFWNLVNWAFVAEQFEGKTYKV 197
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain C from PDB  Type:PROTEIN  Length:195
 aligned with SODF_PSEPU | P09223 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:195
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191     
           SODF_PSEPU     2 AFELPPLPYAHDALQPHISKETLEFHHDKHHNTYVVNLNNLVPGTEFEGKTLEEIVKTSSGGIFNNAAQVWNHTFYWNCLAPNAGGQPTGALADAINAAFGSFDKFKEEFTKTSVGTFGSGWGWLVKKADGSLALASTIGAGCPLTSGDTPLLTCDVWEHAYYIDYRNLRPKYVEAFWNLVNWAFVAEQFEGKTF 196
               SCOP domains d1dt0c1 C:1-83 Fe superoxide dismutase (FeSOD)                                     d1dt0c2 C:84-195 Fe superoxide dismutase (FeSOD)                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee...hhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  -------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dt0 C   1 AFELPPLPYAHDALQPHISKETLEFHHDKHHNTYVVNLNNLVPGTEFEGKTLEEIVKTSSGGIFNNAAQVWNHTFYWNCLSPNAGGQPTGALADAINAAFGSFDKFKEEFTKTSVGTFGSGWGWLVKKADGSLALASTIGAGCPLTIGDTPLLTCDVWEHAYYIDYRNLRPKYVEAFWNLVNWAFVAEQFEGKTY 195
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

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 '\|'

(no "CATH Domain" information available for 1DT0)

(no "Pfam Domain" information available for 1DT0)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (SODF_PSEPU | P09223)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0004784	superoxide dismutase activity	Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + hydrogen peroxide.
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.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		FE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gln A:15 - Pro A:16	[ RasMol ]
		Gln B:15 - Pro B:16	[ RasMol ]
		Gln C:15 - Pro C:16	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1dt0
		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
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	SODF_PSEPU \| P09223
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	1.15.1.1
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	SODF_PSEPU \| P09223
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	SODF_PSEPU \| P09223	:	3sdp

1ar4	SUPEROXIDE DISMUTASE FROM PROPIONIBACTERIUM SHERMANII ACTIVE WITH FE OR MN
1ids	IRON-DEPENDENT SUPEROXIDE DISMUTASE FROM MYCOBACTERIUM TUBERCULOSIS AT 2.0 ANGSTROMS RESOLUTIONS REVEALS NOVEL DIMER-DIMER INTERACTIONS
1isb	STRUCTURE-FUNCTION IN E. COLI IRON SUPEROXIDE DISMUTASE: COMPARISONS WITH THE MANGANESE ENZYME FROM T. THERMOPHILUS
1isc	IRON(III) SUPEROXIDE DISMUTASE (E.C. 1.15.1.1) COMPLEXED WITH AZIDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 6)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File