1O9R - JenaLib

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Title :   THE X-RAY CRYSTAL STRUCTURE OF AGROBACTERIUM TUMEFACIENS DPS, A MEMBER OF THE FAMILY THAT PROTECT DNA WITHOUT BINDING

Authors :   A. Ilari, P. Ceci, E. Chiancone

Date :   18 Dec 02 (Deposition) - 29 May 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.45

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

Keywords :   Iron-Binding Protein, Dna Protection From Oxidative Damage, Dna-Binding, Iron- Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Ceci, A. Ilari, E. Falvo, E. Chiancone
The Dps Protein Of Agrobacterium Tumefaciens Does Not Bind To Dna But Protects It Toward Oxidative Cleavage: X-Ray Crystal Structure, Iron Binding, And Hydroxyl-Radical Scavenging Properties
J. Biol. Chem. V. 278 20319 2003
PubMed-ID: 12660233 | Reference-DOI: 10.1074/JBC.M302114200
(for further references see the PDB file header)

Molecule 1 - AGROBACTERIUM TUMEFACIENS DPS
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11-A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	AGROBACTERIUM TUMEFACIENS
	Organism Taxid	:	358
	Strain	:	GV3101
	Synonym	:	DNA-BINDING PROTEIN, DPS-AT

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (2x)	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	FE	6	Ligand/Ion	FE (III) ION
3	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	FE	-1	Ligand/Ion	FE (III) ION
3	TRS	4	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:67 , GLU A:71 , HIS B:40 , HOH B:2036 , HOH B:2045	BINDING SITE FOR RESIDUE FE A1163
2	AC2	SOFTWARE	HIS A:40 , HOH A:2041 , HOH A:2046 , ASP B:67 , GLU B:71	BINDING SITE FOR RESIDUE FE B1163
3	AC3	SOFTWARE	HIS C:40 , ASP C:67 , GLU C:71 , HOH C:2032 , HOH C:2037	BINDING SITE FOR RESIDUE FE C1163
4	AC4	SOFTWARE	HIS D:40 , ASP D:67 , GLU D:71 , HOH D:2036 , HOH D:2048	BINDING SITE FOR RESIDUE FE D1163
5	AC5	SOFTWARE	ASP E:67 , GLU E:71 , HOH E:2050 , HIS F:40 , HOH F:2034 , HOH F:2043	BINDING SITE FOR RESIDUE FE E1163
6	AC6	SOFTWARE	HIS E:40 , HOH E:2028 , HOH E:2035 , ASP F:67 , GLU F:71 , HOH F:2057	BINDING SITE FOR RESIDUE FE F1163
7	AC7	SOFTWARE	ASP B:138 , HOH B:2132 , HOH B:2133 , HOH B:2134 , ASP D:138 , ASP F:138 , ARG F:145	BINDING SITE FOR RESIDUE TRS B1164
8	AC8	SOFTWARE	ILE D:30 , ARG D:59 , ASP D:63 , ASP D:67 , HOH D:2115	BINDING SITE FOR RESIDUE EDO D1164
9	AC9	SOFTWARE	ASP A:138 , ASP C:138 , ASP E:138 , HOH E:2114 , HOH E:2115 , HOH E:2116	BINDING SITE FOR RESIDUE TRS E1164

(no "SS Bond" information available for 1O9R)

(no "Cis Peptide Bond" information available for 1O9R)

(no "SAP(SNP)/Variant" information available for 1O9R)

Asymmetric Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DPS_1	PS00818	Dps protein family signature 1.	DPS_AGRFC	40-56	6	A:40-56 B:40-56 C:40-56 D:40-56 E:40-56 F:40-56

Biological Unit 1 (1, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DPS_1	PS00818	Dps protein family signature 1.	DPS_AGRFC	40-56	12	A:40-56 B:40-56 C:40-56 D:40-56 E:40-56 F:40-56

(no "Exon" information available for 1O9R)

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:162
 aligned with DPS_AGRFC | Q8UCK6 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
            DPS_AGRFC     1 MKTHKTKNDLPSNAKSTVIGILNESLASVIDLALVTKQAHWNLKGPQFIAVHELLDTFRTQLDNHGDTIAERVVQLGGTALGSLQAVSSTTKLKAYPTDIYKIHDHLDALIERYGEVANMIRKAIDDSDEAGDPTTADIFTAASRDLDKSLWFLEAHVQEKS 162
               SCOP domains d1o9ra_ A: Dodecameric ferritin homolog                                                                                                                            SCOP domains
               CATH domains 1o9rA00 A:1-162  [code=1.20.1260.10, no name defined]                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------DPS_1            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1o9r A   1 MKTHKTKNDLPSNAKSTVIGILNESLASVIDLALVTKQAHWNLKGPQFIAVHELLDTFRTQLDNHGDTIAERVVQLGGTALGSLQAVSSTTKLKAYPTDIYKIHDHLDALIERYGEVANMIRKAIDDSDEAGDPTTADIFTAASRDLDKSLWFLEAHVQEKS 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain B from PDB  Type:PROTEIN  Length:162
 aligned with DPS_AGRFC | Q8UCK6 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
            DPS_AGRFC     1 MKTHKTKNDLPSNAKSTVIGILNESLASVIDLALVTKQAHWNLKGPQFIAVHELLDTFRTQLDNHGDTIAERVVQLGGTALGSLQAVSSTTKLKAYPTDIYKIHDHLDALIERYGEVANMIRKAIDDSDEAGDPTTADIFTAASRDLDKSLWFLEAHVQEKS 162
               SCOP domains d1o9rb_ B: Dodecameric ferritin homolog                                                                                                                            SCOP domains
               CATH domains 1o9rB00 B:1-162  [code=1.20.1260.10, no name defined]                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------DPS_1            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1o9r B   1 MKTHKTKNDLPSNAKSTVIGILNESLASVIDLALVTKQAHWNLKGPQFIAVHELLDTFRTQLDNHGDTIAERVVQLGGTALGSLQAVSSTTKLKAYPTDIYKIHDHLDALIERYGEVANMIRKAIDDSDEAGDPTTADIFTAASRDLDKSLWFLEAHVQEKS 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain C from PDB  Type:PROTEIN  Length:159
 aligned with DPS_AGRFC | Q8UCK6 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:159
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153         
            DPS_AGRFC     4 HKTKNDLPSNAKSTVIGILNESLASVIDLALVTKQAHWNLKGPQFIAVHELLDTFRTQLDNHGDTIAERVVQLGGTALGSLQAVSSTTKLKAYPTDIYKIHDHLDALIERYGEVANMIRKAIDDSDEAGDPTTADIFTAASRDLDKSLWFLEAHVQEKS 162
               SCOP domains d1o9rc_ C: Dodecameric ferritin homolog                                                                                                                         SCOP domains
               CATH domains 1o9rC00 C:4-162  [code=1.20.1260.10, no name defined]                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------DPS_1            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o9r C   4 HKTKNDLPSNAKSTVIGILNESLASVIDLALVTKQAHWNLKGPQFIAVHELLDTFRTQLDNHGDTIAERVVQLGGTALGSLQAVSSTTKLKAYPTDIYKIHDHLDALIERYGEVANMIRKAIDDSDEAGDPTTADIFTAASRDLDKSLWFLEAHVQEKS 162
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153

Chain D from PDB  Type:PROTEIN  Length:160
 aligned with DPS_AGRFC | Q8UCK6 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:160
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162
            DPS_AGRFC     3 THKTKNDLPSNAKSTVIGILNESLASVIDLALVTKQAHWNLKGPQFIAVHELLDTFRTQLDNHGDTIAERVVQLGGTALGSLQAVSSTTKLKAYPTDIYKIHDHLDALIERYGEVANMIRKAIDDSDEAGDPTTADIFTAASRDLDKSLWFLEAHVQEKS 162
               SCOP domains d1o9rd_ D: Dodecameric ferritin homolog                                                                                                                          SCOP domains
               CATH domains 1o9rD00 D:3-162  [code=1.20.1260.10, no name defined]                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------DPS_1            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o9r D   3 THKTKNDLPSNAKSTVIGILNESLASVIDLALVTKQAHWNLKGPQFIAVHELLDTFRTQLDNHGDTIAERVVQLGGTALGSLQAVSSTTKLKAYPTDIYKIHDHLDALIERYGEVANMIRKAIDDSDEAGDPTTADIFTAASRDLDKSLWFLEAHVQEKS 162
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162

Chain E from PDB  Type:PROTEIN  Length:162
 aligned with DPS_AGRFC | Q8UCK6 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
            DPS_AGRFC     1 MKTHKTKNDLPSNAKSTVIGILNESLASVIDLALVTKQAHWNLKGPQFIAVHELLDTFRTQLDNHGDTIAERVVQLGGTALGSLQAVSSTTKLKAYPTDIYKIHDHLDALIERYGEVANMIRKAIDDSDEAGDPTTADIFTAASRDLDKSLWFLEAHVQEKS 162
               SCOP domains d1o9re_ E: Dodecameric ferritin homolog                                                                                                                            SCOP domains
               CATH domains 1o9rE00 E:1-162  [code=1.20.1260.10, no name defined]                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------DPS_1            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1o9r E   1 MKTHKTKNDLPSNAKSTVIGILNESLASVIDLALVTKQAHWNLKGPQFIAVHELLDTFRTQLDNHGDTIAERVVQLGGTALGSLQAVSSTTKLKAYPTDIYKIHDHLDALIERYGEVANMIRKAIDDSDEAGDPTTADIFTAASRDLDKSLWFLEAHVQEKS 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain F from PDB  Type:PROTEIN  Length:162
 aligned with DPS_AGRFC | Q8UCK6 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
            DPS_AGRFC     1 MKTHKTKNDLPSNAKSTVIGILNESLASVIDLALVTKQAHWNLKGPQFIAVHELLDTFRTQLDNHGDTIAERVVQLGGTALGSLQAVSSTTKLKAYPTDIYKIHDHLDALIERYGEVANMIRKAIDDSDEAGDPTTADIFTAASRDLDKSLWFLEAHVQEKS 162
               SCOP domains d1o9rf_ F: Dodecameric ferritin homolog                                                                                                                            SCOP domains
               CATH domains 1o9rF00 F:1-162  [code=1.20.1260.10, no name defined]                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------DPS_1            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1o9r F   1 MKTHKTKNDLPSNAKSTVIGILNESLASVIDLALVTKQAHWNLKGPQFIAVHELLDTFRTQLDNHGDTIAERVVQLGGTALGSLQAVSSTTKLKAYPTDIYKIHDHLDALIERYGEVANMIRKAIDDSDEAGDPTTADIFTAASRDLDKSLWFLEAHVQEKS 162
                                    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(

)

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)

Agrobacterium tumefaciens, Dps [TaxId: 358] (1)

1a	d1o9ra_	A:
1b	d1o9rb_	B:
1c	d1o9rc_	C:
1d	d1o9rd_	D:
1e	d1o9re_	E:
1f	d1o9rf_	F:

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)

Agrobacterium tumefaciens. Organism_taxid: 358. Strain: gv3101. (1)

1a	1o9rA00	A:1-162
1b	1o9rB00	B:1-162
1c	1o9rE00	E:1-162
1d	1o9rF00	F:1-162
1e	1o9rD00	D:3-162
1f	1o9rC00	C:4-162

(no "Pfam Domain" information available for 1O9R)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (DPS_AGRFC | Q8UCK6)

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.
	GO:0016722	oxidoreductase activity, oxidizing metal ions	Catalysis of an oxidation-reduction in which the oxidation state of metal ion is altered.
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.

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	1o9r
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 6)

Exons (0, 0)

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