1Y07 - 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)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE SUPEROXIDE REDUCTASE FROM TREPONEMA PALLIDUM

Authors :   T. Santos-Silva, J. Trincao, A. L. Carvalho, C. Bonifacio, F. Auchere, J. Moura, M. J. Romao

Date :   15 Nov 04 (Deposition) - 22 Nov 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

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

Keywords :   Beta-Sheet, Iron Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Santos-Silva, J. Trincao, A. L. Carvalho, C. Bonifacio, F. Auchere, P. Raleiras, I. Moura, J. Moura, M. J. Romao
The First Crystal Structure Of Class Iii Superoxide Reductase From Treponema Pallidum.
J. Biol. Inorg. Chem. V. 11 548 2006
PubMed-ID: 16791639 | Reference-DOI: 10.1007/S00775-006-0104-Y
(for further references see the PDB file header)

Molecule 1 - DESULFOFERRODOXIN (RBO)
	Chains	:	A, B, C, D
	EC Number	:	1.15.1.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PT7-7
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	TP0823
	Organism Scientific	:	TREPONEMA PALLIDUM SUBSP. PALLIDUM STR. NICHOLS
	Organism Taxid	:	243276
	Strain	:	SUBSP. PALLIDUM STR. NICHOLS
	Synonym	:	SUPEROXIDE REDUCTASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 7)

No.	Name	Count	Type	Full Name
1	FE	5	Ligand/Ion	FE (III) ION
2	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (0, 0)

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

Biological Unit 2 (0, 0)

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

Biological Unit 3 (0, 0)

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

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:50 , HIS A:70 , HIS A:76 , CYS A:119 , HIS A:122	BINDING SITE FOR RESIDUE FE A 130
2	AC2	SOFTWARE	HIS B:50 , HIS B:70 , HIS B:76 , CYS B:119 , HIS B:122	BINDING SITE FOR RESIDUE FE B 130
3	AC3	SOFTWARE	HIS C:50 , HIS C:70 , HIS C:76 , CYS C:119 , HIS C:122	BINDING SITE FOR RESIDUE FE C 130
4	AC4	SOFTWARE	HIS D:50 , HIS D:70 , HIS D:76 , CYS D:119 , HIS D:122 , HOH D:192	BINDING SITE FOR RESIDUE FE D 130
5	AC5	SOFTWARE	ALA A:108 , HOH A:513 , HOH A:550 , HOH A:551 , HOH C:520 , HOH C:522	BINDING SITE FOR RESIDUE MG A 501
6	AC6	SOFTWARE	HOH A:538 , ALA C:108 , HOH C:518 , HOH C:525 , HOH C:526 , HOH C:542	BINDING SITE FOR RESIDUE MG C 502
7	AC7	SOFTWARE	GLN A:111 , GLN C:111	BINDING SITE FOR RESIDUE FE A 503

(no "SS Bond" information available for 1Y07)

Asymmetric Unit

No.	Residues
1	Val A:65	-	Gly A:66
2	Val C:65	-	Gly C:66

(no "SAP(SNP)/Variant" information available for 1Y07)

(no "PROSITE Motif" information available for 1Y07)

(no "Exon" information available for 1Y07)

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:121
 aligned with O83795_TREPA | O83795 from UniProtKB/TrEMBL  Length:128

    Alignment length:126
                                    12        22        32        42        52        62        72        82        92       102       112       122      
         O83795_TREPA     3 RELSFFLQKESAGFFLGMDAPAGSSVACGSEVLRAVPVGTVDAAKEKHIPVVEVHGHEVKVKVGSVAHPMTPEHYIAWVCLKTRKGIQLKELPVDGAPEVTFALTADDQVLEAYEFCNLHGVWSGK 128
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee..-----.eeee......eeee..eeee.........hhhhhheeeeee..eeeeee............eeeeeeee...eeeee.......eeeee......eeeeeeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1y07 A   3 RELSFFLQ-----FFLGMDAPAGSSVACGSEVLRAVPVGTVDAAKEKHIPVVEVHGHEVKVKVGSVAHPMTPEHYIAWVCLKTRKGIQLKELPVDGAPEVTFALTADDQVLEAYEFCNLHGVWSGK 128
                                   | -   |    22        32        42        52        62        72        82        92       102       112       122      
                                  10    16

Chain B from PDB  Type:PROTEIN  Length:122
 aligned with O83795_TREPA | O83795 from UniProtKB/TrEMBL  Length:128

    Alignment length:127
                                    11        21        31        41        51        61        71        81        91       101       111       121       
         O83795_TREPA     2 GRELSFFLQKESAGFFLGMDAPAGSSVACGSEVLRAVPVGTVDAAKEKHIPVVEVHGHEVKVKVGSVAHPMTPEHYIAWVCLKTRKGIQLKELPVDGAPEVTFALTADDQVLEAYEFCNLHGVWSGK 128
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.---..eeeee......eee....eee.....--..hhhhhheeeeee..eeeeee............eeeeeeee..eeeeee.......eeeee......eeeeeeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y07 B   2 GRELSFFLQ---AGFFLGMDAPAGSSVACGSEVLRAVPVG--DAAKEKHIPVVEVHGHEVKVKVGSVAHPMTPEHYIAWVCLKTRKGIQLKELPVDGAPEVTFALTADDQVLEAYEFCNLHGVWSGK 128
                                    |-  |     21        31        41  |     51        61        71        81        91       101       111       121       
                                   10  14                         41 44

Chain C from PDB  Type:PROTEIN  Length:124
 aligned with O83795_TREPA | O83795 from UniProtKB/TrEMBL  Length:128

    Alignment length:128
                                    10        20        30        40        50        60        70        80        90       100       110       120        
         O83795_TREPA     1 MGRELSFFLQKESAGFFLGMDAPAGSSVACGSEVLRAVPVGTVDAAKEKHIPVVEVHGHEVKVKVGSVAHPMTPEHYIAWVCLKTRKGIQLKELPVDGAPEVTFALTADDQVLEAYEFCNLHGVWSGK 128
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee......eeeee......eeee..eeee.....----hhhhhheeeeee..eeeeee............eeeeeeee..eeeeee.......eeeee......eeeeeeee...eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y07 C   1 MGRELSFFLQKESAGFFLGMDAPAGSSVACGSEVLRAVPVG----AKEKHIPVVEVHGHEVKVKVGSVAHPMTPEHYIAWVCLKTRKGIQLKELPVDGAPEVTFALTADDQVLEAYEFCNLHGVWSGK 128
                                    10        20        30        40|    |  50        60        70        80        90       100       110       120        
                                                                   41   46

Chain D from PDB  Type:PROTEIN  Length:123
 aligned with O83795_TREPA | O83795 from UniProtKB/TrEMBL  Length:128

    Alignment length:127
                                    11        21        31        41        51        61        71        81        91       101       111       121       
         O83795_TREPA     2 GRELSFFLQKESAGFFLGMDAPAGSSVACGSEVLRAVPVGTVDAAKEKHIPVVEVHGHEVKVKVGSVAHPMTPEHYIAWVCLKTRKGIQLKELPVDGAPEVTFALTADDQVLEAYEFCNLHGVWSGK 128
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------Des    ulfoferrodox-1y07D01 D:42-128                                                    Pfam domains (1)
           Pfam domains (2) ----------------------------------------Des    ulfoferrodox-1y07D02 D:42-128                                                    Pfam domains (2)
           Pfam domains (3) ----------------------------------------Des    ulfoferrodox-1y07D03 D:42-128                                                    Pfam domains (3)
           Pfam domains (4) ----------------------------------------Des    ulfoferrodox-1y07D04 D:42-128                                                    Pfam domains (4)
         Sec.struct. author ...eeeee......eeeee......eeee..eeee...ee...----...eeeeee..eeeeee............eeeeeeee..eeeeee.......eeeee......eeeeeeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y07 D   2 GRELSFFLQKESAGFFLGMDAPAGSSVACGSEVLRAVPVGTVD----KHIPVVEVHGHEVKVKVGSVAHPMTPEHYIAWVCLKTRKGIQLKELPVDGAPEVTFALTADDQVLEAYEFCNLHGVWSGK 128
                                    11        21        31        41  |    |51        61        71        81        91       101       111       121       
                                                                     44   49

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 "SCOP Domain" information available for 1Y07)

(no "CATH Domain" information available for 1Y07)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: SOR (12)

Family: Desulfoferrodox (8)

Treponema pallidum (1)

1a	Desulfoferrodox-1y07D01	D:42-128
1b	Desulfoferrodox-1y07D02	D:42-128
1c	Desulfoferrodox-1y07D03	D:42-128
1d	Desulfoferrodox-1y07D04	D:42-128

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (O83795_TREPA | O83795)

molecular function
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	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:0050605	superoxide reductase activity	Catalysis of the reaction: superoxide + reduced rubredoxin + 2 H+ = H2O2 + rubredoxin.
biological process
	GO:0098869	cellular oxidant detoxification	Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
	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.

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 ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Val A:65 - Gly A:66	[ RasMol ]
		Val C:65 - Gly C:66	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ 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 \| Biol. Unit 3 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
	1y07
		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
	O83795_TREPA \| O83795
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	1.15.1.2
		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
	O83795_TREPA \| O83795
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1Y07)

(no "Related Entries Specified in the PDB File" available for 1Y07)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 4)

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