1TJO - JenaLib

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Title :   IRON-OXO CLUSTERS BIOMINERALIZING ON PROTEIN SURFACES. STRUCTURAL ANALYSIS OF H.SALINARUM DPSA IN ITS LOW AND HIGH IRON STATES

Authors :   K. Zeth, S. Offermann, L. O. Essen, D. Oesterhelt

Date :   07 Jun 04 (Deposition) - 19 Oct 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Dpsa, Ferritin, Low-Iron, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Zeth, S. Offermann, L. O. Essen, D. Oesterhelt
Iron-Oxo Clusters Biomineralizing On Protein Surfaces: Structural Analysis Of Halobacterium Salinarum Dpsa In Its Low- And High-Iron States.
Proc. Natl. Acad. Sci. Usa V. 101 13780 2004
PubMed-ID: 15365182 | Reference-DOI: 10.1073/PNAS.0401821101

Molecule 1 - IRON-RICH DPSA-HOMOLOG PROTEIN
	Chains	:	A, B, C, D
	Organism Scientific	:	HALOBACTERIUM SALINARUM
	Organism Taxid	:	2242
	Strain	:	WILDTYPE STRAIN - TOM
	Synonym	:	BACTERIOFERRITIN DPSA

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 14)

No.	Name	Count	Type	Full Name
1	FE	6	Ligand/Ion	FE (III) ION
2	MG	4	Ligand/Ion	MAGNESIUM ION
3	NA	2	Ligand/Ion	SODIUM ION
4	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	NA	-1	Ligand/Ion	SODIUM ION
4	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:150 , ARG A:153 , HIS C:150 , ARG C:153 , HIS D:150 , ARG D:153	BINDING SITE FOR RESIDUE SO4 A 1201
02	AC2	SOFTWARE	HIS B:150 , ARG B:153	BINDING SITE FOR RESIDUE SO4 B 1202
03	AC3	SOFTWARE	HIS A:52 , ASP B:79 , GLU B:83 , HOH B:1421 , HOH B:1589	BINDING SITE FOR RESIDUE FE B 1301
04	AC4	SOFTWARE	ASP A:79 , GLU A:83 , HOH A:1477 , HOH A:1547 , HIS B:52	BINDING SITE FOR RESIDUE FE A 1302
05	AC5	SOFTWARE	HIS C:52 , HOH C:1628 , ASP D:79 , GLU D:83 , HOH D:1648	BINDING SITE FOR RESIDUE FE D 1303
06	AC6	SOFTWARE	ASP C:79 , GLU C:83 , HOH C:1540 , HOH C:1645 , HIS D:52	BINDING SITE FOR RESIDUE FE C 1304
07	AC7	SOFTWARE	GLU B:154 , HOH B:1479 , HOH B:1610	BINDING SITE FOR RESIDUE FE B 1305
08	AC8	SOFTWARE	GLU A:154 , HOH A:1546 , HOH A:1569 , GLU C:154 , HOH C:1642 , HOH C:1678 , HOH C:1706 , GLU D:154 , HOH D:1649	BINDING SITE FOR RESIDUE FE A 1306
09	AC9	SOFTWARE	GLN A:86 , GLU B:56 , HIS D:168 , HOH D:1566 , HOH D:1647 , HOH D:1669	BINDING SITE FOR RESIDUE MG D 1401
10	BC1	SOFTWARE	HIS A:168 , GLN C:86 , HOH C:1644 , GLU D:56 , HOH D:1624 , HOH D:1670	BINDING SITE FOR RESIDUE MG A 1402
11	BC2	SOFTWARE	GLU A:56 , GLN B:86 , HIS B:168 , HOH B:1523 , HOH B:1572 , HOH B:1592	BINDING SITE FOR RESIDUE MG B 1403
12	BC3	SOFTWARE	GLU C:56 , HIS C:168 , HOH C:1606 , HOH C:1643 , HOH C:1654 , GLN D:86	BINDING SITE FOR RESIDUE MG C 1404
13	BC4	SOFTWARE	GLU A:59 , GLU B:59 , GLU D:59	BINDING SITE FOR RESIDUE NA D 1501
14	BC5	SOFTWARE	GLU C:59	BINDING SITE FOR RESIDUE NA C 1502

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

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

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

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

(no "Exon" information available for 1TJO)

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:180
 aligned with DPS_HALSA | Q9HMP7 from UniProtKB/Swiss-Prot  Length:182

    Alignment length:180
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
            DPS_HALSA     2 STQKNARATAGEVEGSDALRMDADRAEQCVDALNADLANVYVLYHQLKKHHWNVEGAEFRDLHLFLGEAAETAEEVADELAERVQALGGVPHASPETLQAEASVDVEDEDVYDIRTSLANDMAIYGDIIEATREHTELAENLGDHATAHMLREGLIELEDDAHHIEHYLEDDTLVTQGAL 181
               SCOP domains d1tjoa_ A: Dodecameric ferritin homolog                                                                                                                                              SCOP domains
               CATH domains 1tjoA00 A:2-181  [code=1.20.1260.10, no name defined]                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tjo A   2 STQKNARATAGEVEGSDALRMDADRAEQCVDALNADLANVYVLYHQLKKHHWNVEGAEFRDLHLFLGEAAETAEEVADELAERVQALGGVPHASPETLQAEASVDVEDEDVYDIRTSLANDMAIYGDIIEATREHTELAENLGDHATAHMLREGLIELEDDAHHIEHYLEDDTLVTQGAL 181
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181

Chain B from PDB  Type:PROTEIN  Length:175
 aligned with DPS_HALSA | Q9HMP7 from UniProtKB/Swiss-Prot  Length:182

    Alignment length:175
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176     
            DPS_HALSA     7 ARATAGEVEGSDALRMDADRAEQCVDALNADLANVYVLYHQLKKHHWNVEGAEFRDLHLFLGEAAETAEEVADELAERVQALGGVPHASPETLQAEASVDVEDEDVYDIRTSLANDMAIYGDIIEATREHTELAENLGDHATAHMLREGLIELEDDAHHIEHYLEDDTLVTQGAL 181
               SCOP domains d1tjob_ B: Dodecameric ferritin homolog                                                                                                                                         SCOP domains
               CATH domains 1tjoB00 B:7-181  [code=1.20.1260.10, no name defined]                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tjo B   7 ARATAGEVEGSDALRMDADRAEQCVDALNADLANVYVLYHQLKKHHWNVEGAEFRDLHLFLGEAAETAEEVADELAERVQALGGVPHASPETLQAEASVDVEDEDVYDIRTSLANDMAIYGDIIEATREHTELAENLGDHATAHMLREGLIELEDDAHHIEHYLEDDTLVTQGAL 181
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176

Chain C from PDB  Type:PROTEIN  Length:175
 aligned with DPS_HALSA | Q9HMP7 from UniProtKB/Swiss-Prot  Length:182

    Alignment length:175
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176     
            DPS_HALSA     7 ARATAGEVEGSDALRMDADRAEQCVDALNADLANVYVLYHQLKKHHWNVEGAEFRDLHLFLGEAAETAEEVADELAERVQALGGVPHASPETLQAEASVDVEDEDVYDIRTSLANDMAIYGDIIEATREHTELAENLGDHATAHMLREGLIELEDDAHHIEHYLEDDTLVTQGAL 181
               SCOP domains d1tjoc_ C: Dodecameric ferritin homolog                                                                                                                                         SCOP domains
               CATH domains 1tjoC00 C:7-181  [code=1.20.1260.10, no name defined]                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tjo C   7 ARATAGEVEGSDALRMDADRAEQCVDALNADLANVYVLYHQLKKHHWNVEGAEFRDLHLFLGEAAETAEEVADELAERVQALGGVPHASPETLQAEASVDVEDEDVYDIRTSLANDMAIYGDIIEATREHTELAENLGDHATAHMLREGLIELEDDAHHIEHYLEDDTLVTQGAL 181
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176

Chain D from PDB  Type:PROTEIN  Length:175
 aligned with DPS_HALSA | Q9HMP7 from UniProtKB/Swiss-Prot  Length:182

    Alignment length:175
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176     
            DPS_HALSA     7 ARATAGEVEGSDALRMDADRAEQCVDALNADLANVYVLYHQLKKHHWNVEGAEFRDLHLFLGEAAETAEEVADELAERVQALGGVPHASPETLQAEASVDVEDEDVYDIRTSLANDMAIYGDIIEATREHTELAENLGDHATAHMLREGLIELEDDAHHIEHYLEDDTLVTQGAL 181
               SCOP domains d1tjod_ D: Dodecameric ferritin homolog                                                                                                                                         SCOP domains
               CATH domains 1tjoD00 D:7-181  [code=1.20.1260.10, no name defined]                                                                                                                           CATH domains
           Pfam domains (1) ------------------------Ferritin-1tjoD01 D:31-176                                                                                                                         ----- Pfam domains (1)
           Pfam domains (2) ------------------------Ferritin-1tjoD02 D:31-176                                                                                                                         ----- Pfam domains (2)
           Pfam domains (3) ------------------------Ferritin-1tjoD03 D:31-176                                                                                                                         ----- Pfam domains (3)
           Pfam domains (4) ------------------------Ferritin-1tjoD04 D:31-176                                                                                                                         ----- Pfam domains (4)
         Sec.struct. author ................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tjo D   7 ARATAGEVEGSDALRMDADRAEQCVDALNADLANVYVLYHQLKKHHWNVEGAEFRDLHLFLGEAAETAEEVADELAERVQALGGVPHASPETLQAEASVDVEDEDVYDIRTSLANDMAIYGDIIEATREHTELAENLGDHATAHMLREGLIELEDDAHHIEHYLEDDTLVTQGAL 181
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176

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 alpha proteins (14657)

Fold: Ferritin-like (533)

Superfamily: Ferritin-like (489)

Family: Ferritin (232)

Protein domain: Dodecameric ferritin homolog (44)

Halobacterium salinarum [TaxId: 2242] (5)

1a	d1tjoa_	A:
1b	d1tjob_	B:
1c	d1tjoc_	C:
1d	d1tjod_	D:

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)

Halobacterium salinarum. Organism_taxid: 2242. Strain: wildtype strain- tom (1)

1a	1tjoB00	B:7-181
1b	1tjoC00	C:7-181
1c	1tjoD00	D:7-181
1d	1tjoA00	A:2-181

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ferritin (185)

Family: Ferritin (83)

Halobacterium salinarium (strain ATCC 700922 / JCM 11081 / NRC-1) (Halobacterium halobium) (5)

1a	Ferritin-1tjoD01	D:31-176
1b	Ferritin-1tjoD02	D:31-176
1c	Ferritin-1tjoD03	D:31-176
1d	Ferritin-1tjoD04	D:31-176

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (DPS_HALSA | Q9HMP7)

molecular function
	GO:0008199	ferric iron binding	Interacting selectively and non-covalently with ferric iron, Fe(III).
	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: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:0006950	response to stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 14)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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