2I7F - JenaLib

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Title :   SPHINGOMONAS YANOIKUYAE B1 FERREDOXIN

Authors :   S. Ramaswamy, E. N. Brown

Date :   30 Aug 06 (Deposition) - 20 Mar 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Rieske Ferredoxin, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. J. Ferraro, E. N. Brown, C. L. Yu, R. E. Parales, D. T. Gibson, S. Ramaswamy
Structural Investigations Of The Ferredoxin And Terminal Oxygenase Components Of The Biphenyl 2, 3-Dioxygenase From Sphingobium Yanoikuyae B1.
Bmc Struct. Biol. V. 7 10 2007
PubMed-ID: 17349044 | Reference-DOI: 10.1186/1472-6807-7-10
(for further references see the PDB file header)

Molecule 1 - FERREDOXIN COMPONENT OF DIOXYGENASE
	Chains	:	A, B
	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	:	AHDA3
	Organism Scientific	:	SPHINGOBIUM YANOIKUYAE
	Organism Taxid	:	13690
	Strain	:	B1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	CIT	2	Ligand/Ion	CITRIC ACID
2	FES	2	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	FES	1	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	FES	1	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
3	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:8 , GLN A:9 , SER A:12 , TRP A:98 , HOH A:550	BINDING SITE FOR RESIDUE SO4 A 500
2	AC2	SOFTWARE	CYS A:45 , HIS A:47 , GLY A:48 , CYS A:64 , PHE A:66 , HIS A:67 , CYS A:83	BINDING SITE FOR RESIDUE FES A 501
3	AC3	SOFTWARE	CYS B:45 , HIS B:47 , GLY B:48 , CYS B:64 , PHE B:66 , HIS B:67 , CYS B:83	BINDING SITE FOR RESIDUE FES B 502
4	AC4	SOFTWARE	ASN A:49 , HOH A:515 , HOH A:523 , HOH A:563 , HOH A:564 , HOH A:579	BINDING SITE FOR RESIDUE CIT A 503
5	AC5	SOFTWARE	ALA A:77 , ALA A:78 , GLN A:84 , PRO A:86 , THR B:89 , PRO B:91 , HOH B:515 , HOH B:546	BINDING SITE FOR RESIDUE CIT B 504

(no "SS Bond" information available for 2I7F)

Asymmetric Unit

No.	Residues
1	Phe A:81	-	Pro A:82
2	Phe B:81	-	Pro B:82

(no "SAP(SNP)/Variant" information available for 2I7F)

(no "PROSITE Motif" information available for 2I7F)

(no "Exon" information available for 2I7F)

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
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Chain A from PDB  Type:PROTEIN  Length:102
 aligned with A2TC31_SPHYA | A2TC31 from UniProtKB/TrEMBL  Length:108

    Alignment length:102
                                    12        22        32        42        52        62        72        82        92       102  
         A2TC31_SPHYA     3 NKLRLCQVASVKDGEPVAVYQEKMPALAVYNVDGEVFVTDNLCTHGNAMLTDGYQDGTIIECPFHGGSFDIATGAAKAFPCQIPIKTYPVTIEDGWVCIDQP 104
               SCOP domains d2i7fa_ A: automated matches                                                                           SCOP domains
               CATH domains 2i7fA00 A:3-104 'Rieske'-like iron-sulphur domains                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.hhh.....eee.......eeeeee..eeeeee........hhhhheee..eee......eee................ee.eeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 2i7f A   3 NKLRLCQVASVKDGEPVAVYQEKMPALAVYNVDGEVFVTDNLCTHGNAMLTDGYQDGTIIECPFHGGSFDIATGAAKAFPCQIPIKTYPVTIEDGWVCIDQP 104
                                    12        22        32        42        52        62        72        82        92       102

Chain B from PDB  Type:PROTEIN  Length:102
 aligned with A2TC31_SPHYA | A2TC31 from UniProtKB/TrEMBL  Length:108

    Alignment length:102
                                    12        22        32        42        52        62        72        82        92       102  
         A2TC31_SPHYA     3 NKLRLCQVASVKDGEPVAVYQEKMPALAVYNVDGEVFVTDNLCTHGNAMLTDGYQDGTIIECPFHGGSFDIATGAAKAFPCQIPIKTYPVTIEDGWVCIDQP 104
               SCOP domains d2i7fb_ B: automated matches                                                                           SCOP domains
               CATH domains 2i7fB00 B:3-104 'Rieske'-like iron-sulphur domains                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee.hhh.....eee.......eeeeee..eeeeee........hhhhheee..eee......eee................ee..eee..eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 2i7f B   3 NKLRLCQVASVKDGEPVAVYQEKMPALAVYNVDGEVFVTDNLCTHGNAMLTDGYQDGTIIECPFHGGSFDIATGAAKAFPCQIPIKTYPVTIEDGWVCIDQP 104
                                    12        22        32        42        52        62        72        82        92       102

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

)

Organisms( (-)

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Class: All beta proteins (24004)

Fold: ISP domain (115)

Superfamily: ISP domain (115)

Family: automated matches (22)

Protein domain: automated matches (22)

Sphingobium yanoikuyae [TaxId: 13690] (3)

1a	d2i7fa_	A:
1b	d2i7fb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: 3-layer Sandwich (102)

Topology: Rieske Iron-sulfur Protein (99)

Homologous Superfamily: 'Rieske'-like iron-sulphur domains (99)

Sphingobium yanoikuyae. Organism_taxid: 13690. Strain: b1. (1)

1a	2i7fA00	A:3-104
1b	2i7fB00	B:3-104

(no "Pfam Domain" information available for 2I7F)

Asymmetric Unit(hide GO term definitions)

Chain A,B (A2TC31_SPHYA | A2TC31)

molecular function
	GO:0051537	2 iron, 2 sulfur cluster binding	Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
	GO:0051213	dioxygenase activity	Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	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.
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.

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1fqt	RIESKE DIOXYGENASE FERREDOXIN
1sjg	RIESKE DIOXYGENASE FERREDOXIN
1vck	RIESKE DIOXYGENASE FERREDOXIN

Description

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Ligands, Modified Residues, Ions (3, 5)

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SS Bonds (0, 0)

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