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Title :   THE 2.6 A STRUCTURE RESOLUTION OF RHODOBACTER CAPSULATUS BACTERIOFERRITIN WITH METAL-FREE DINUCLEAR SITE AND HEME IRON IN A CRYSTALLOGRAPHIC SPECIAL POSITION

Authors :   D. Cobessi, L. -S. Huang, M. Ban, N. G. Pon, F. Daldal, E. A. Berry

Date :   24 Jun 01 (Deposition) - 09 Jan 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B,C  (8x)

Keywords :   Iron Storage Protein, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Cobessi, L. S. Huang, M. Ban, N. G. Pon, F. Daldal, E. A. Berry
The 2. 6 A Resolution Structure Of Rhodobacter Capsulatus Bacterioferritin With Metal-Free Dinuclear Site And Heme Iron In A Crystallographic 'Special Position'.
Acta Crystallogr. , Sect. D V. 58 29 2002
PubMed-ID: 11752777 | Reference-DOI: 10.1107/S0907444901017267

Molecule 1 - BACTERIOFERRITIN
	Chains	:	A, B, C
	Organism Scientific	:	RHODOBACTER CAPSULATUS
	Organism Taxid	:	1061
	Synonym	:	BFR

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (8x)	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	HEM	3	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 1 (1, 24)

No.	Name	Count	Type	Full Name
1	HEM	24	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:19 , TRP A:26 , ARG A:45 , MET A:52 , ALA A:55 , HEM A:201 , LEU B:19 , TRP B:26 , ARG B:45 , MET B:52	BINDING SITE FOR RESIDUE HEM B 200
2	AC2	SOFTWARE	LEU A:19 , TRP A:26 , ARG A:45 , MET A:52 , SER B:23 , TRP B:26 , ARG B:45 , MET B:52 , HEM B:200	BINDING SITE FOR RESIDUE HEM A 201
3	AC3	SOFTWARE	LEU C:19 , ILE C:22 , SER C:23 , TRP C:26 , ARG C:45 , ILE C:49 , MET C:52	BINDING SITE FOR RESIDUE HEM C 202

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

(no "Cis Peptide Bond" information available for 1JGC)

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

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BACTERIOFERRITIN	PS00549	Bacterioferritin signature.	BFR_RHOCA	1-19	3	A:1-19 B:1-19 C:1-19
2	FERRITIN_LIKE	PS50905	Ferritin-like diiron domain profile.	BFR_RHOCA	1-145	3	A:1-145 B:1-145 C:1-145

Biological Unit 1 (2, 48)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BACTERIOFERRITIN	PS00549	Bacterioferritin signature.	BFR_RHOCA	1-19	24	A:1-19 B:1-19 C:1-19
2	FERRITIN_LIKE	PS50905	Ferritin-like diiron domain profile.	BFR_RHOCA	1-145	24	A:1-145 B:1-145 C:1-145

(no "Exon" information available for 1JGC)

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:160
 aligned with BFR_RHOCA | Q59738 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
            BFR_RHOCA     1 MKGDAKVIEFLNAALRSELTAISQYWVHFRLQEDWGLAKMAKKSREESIEEMGHADKIIARILFLEGHPNLQKLDPLRIGEGPRETLECDLAGEHDALKLYREARDYCAEVGDIVSKNIFESLITDEEGHVDFLETQISLYDRLGPQGFALLNAAPMDAA 160
               SCOP domains d1jgca_ A: Bacterioferritin (cytochrome b1)                                                                                                                      SCOP domains
               CATH domains 1jgcA00 A:1-160  [code=1.20.1260.10, no name defined]                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) BACTERIOFERRITIN   --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) FERRITIN_LIKE  PDB: A:1-145 UniProt: 1-145                                                                                                       --------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jgc A   1 MKGDAKVIEFLNAALRSELTAISQYWVHFRLQEDWGLAKMAKKSREESIEEMGHADKIIARILFLEGHPNLQKLDPLRIGEGPRETLECDLAGEHDALKLYREARDYCAEVGDIVSKNIFESLITDEEGHVDFLETQISLYDRLGPQGFALLNAAPMDAA 160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain B from PDB  Type:PROTEIN  Length:160
 aligned with BFR_RHOCA | Q59738 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
            BFR_RHOCA     1 MKGDAKVIEFLNAALRSELTAISQYWVHFRLQEDWGLAKMAKKSREESIEEMGHADKIIARILFLEGHPNLQKLDPLRIGEGPRETLECDLAGEHDALKLYREARDYCAEVGDIVSKNIFESLITDEEGHVDFLETQISLYDRLGPQGFALLNAAPMDAA 160
               SCOP domains d1jgcb_ B: Bacterioferritin (cytochrome b1)                                                                                                                      SCOP domains
               CATH domains 1jgcB00 B:1-160  [code=1.20.1260.10, no name defined]                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) BACTERIOFERRITIN   --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) FERRITIN_LIKE  PDB: B:1-145 UniProt: 1-145                                                                                                       --------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jgc B   1 MKGDAKVIEFLNAALRSELTAISQYWVHFRLQEDWGLAKMAKKSREESIEEMGHADKIIARILFLEGHPNLQKLDPLRIGEGPRETLECDLAGEHDALKLYREARDYCAEVGDIVSKNIFESLITDEEGHVDFLETQISLYDRLGPQGFALLNAAPMDAA 160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain C from PDB  Type:PROTEIN  Length:160
 aligned with BFR_RHOCA | Q59738 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
            BFR_RHOCA     1 MKGDAKVIEFLNAALRSELTAISQYWVHFRLQEDWGLAKMAKKSREESIEEMGHADKIIARILFLEGHPNLQKLDPLRIGEGPRETLECDLAGEHDALKLYREARDYCAEVGDIVSKNIFESLITDEEGHVDFLETQISLYDRLGPQGFALLNAAPMDAA 160
               SCOP domains d1jgcc_ C: Bacterioferritin (cytochrome b1)                                                                                                                      SCOP domains
               CATH domains 1jgcC00 C:1-160  [code=1.20.1260.10, no name defined]                                                                                                            CATH domains
           Pfam domains (1) -------Ferritin-1jgcC01 C:8-144                                                                                                                 ---------------- Pfam domains (1)
           Pfam domains (2) -------Ferritin-1jgcC02 C:8-144                                                                                                                 ---------------- Pfam domains (2)
           Pfam domains (3) -------Ferritin-1jgcC03 C:8-144                                                                                                                 ---------------- Pfam domains (3)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) BACTERIOFERRITIN   --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) FERRITIN_LIKE  PDB: C:1-145 UniProt: 1-145                                                                                                       --------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jgc C   1 MKGDAKVIEFLNAALRSELTAISQYWVHFRLQEDWGLAKMAKKSREESIEEMGHADKIIARILFLEGHPNLQKLDPLRIGEGPRETLECDLAGEHDALKLYREARDYCAEVGDIVSKNIFESLITDEEGHVDFLETQISLYDRLGPQGFALLNAAPMDAA 160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

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(

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Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Ferritin-like (533)

Superfamily: Ferritin-like (489)

Family: Ferritin (232)

Protein domain: Bacterioferritin (cytochrome b1) (19)

Rhodobacter capsulatus [TaxId: 1061] (1)

1a	d1jgca_	A:
1b	d1jgcb_	B:
1c	d1jgcc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Ferritin; (180)

Homologous Superfamily: [code=1.20.1260.10, no name defined] (180)

Rhodobacter capsulatus. Organism_taxid: 1061 (1)

1a	1jgcA00	A:1-160
1b	1jgcB00	B:1-160
1c	1jgcC00	C:1-160

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ferritin (185)

Family: Ferritin (83)

Rhodobacter capsulatus (Rhodopseudomonas capsulata) (1)

1a	Ferritin-1jgcC01	C:8-144
1b	Ferritin-1jgcC02	C:8-144
1c	Ferritin-1jgcC03	C:8-144

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (BFR_RHOCA | Q59738)

molecular function
	GO:0008199	ferric iron binding	Interacting selectively and non-covalently with ferric iron, Fe(III).
	GO:0004322	ferroxidase activity	Catalysis of the reaction: 4 Fe2+ + 4 H+ + O2 = 4 Fe3+ + 2 H2O.
	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:0006879	cellular iron ion homeostasis	Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
	GO:0006826	iron ion transport	The directed movement of iron (Fe) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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.
cellular component
	GO:0005623	cell	The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

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