1JI5 - JenaLib

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Title :   DLP-1 FROM BACILLUS ANTHRACIS

Authors :   E. Papinutto, W. G. Dundon, N. Pitulis, R. Battistutta, C. Montecucco,

Date :   29 Jun 01 (Deposition) - 19 Jun 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Dodecamer, Four-Helix Bundle, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Papinutto, W. G. Dundon, N. Pitulis, R. Battistutta, C. Montecucco G. Zanotti
Structure Of Two Iron-Binding Proteins From Bacillus Anthracis.
J. Biol. Chem. V. 277 15093 2002
PubMed-ID: 11836250 | Reference-DOI: 10.1074/JBC.M112378200
(for further references see the PDB file header)

Molecule 1 - DLP-1
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSM214G
	Expression System Strain	:	XL1-BLUE
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DLP-1
	Organism Scientific	:	BACILLUS ANTHRACIS
	Organism Taxid	:	1392

		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 (2, 5)

No.	Name	Count	Type	Full Name
1	FE	4	Ligand/Ion	FE (III) ION
2	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION
2	MPD	3	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:27 , HOH A:198 , ASP B:54 , GLU B:58	BINDING SITE FOR RESIDUE FE B 151
2	AC2	SOFTWARE	ASP A:54 , GLU A:58 , HIS B:27 , HOH B:2028	BINDING SITE FOR RESIDUE FE A 152
3	AC3	SOFTWARE	HIS C:27 , HOH C:191 , ASP D:54 , GLU D:58	BINDING SITE FOR RESIDUE FE D 153
4	AC4	SOFTWARE	ASP C:54 , GLU C:58 , HIS D:27 , HOH D:192	BINDING SITE FOR RESIDUE FE C 154
5	AC5	SOFTWARE	SER A:17 , PHE A:20 , THR A:21 , ILE A:53 , MET A:71 , HOH A:157 , HOH A:167 , SER B:17 , PHE B:20 , THR B:21 , MET B:71	BINDING SITE FOR RESIDUE MPD B 2001

(no "SS Bond" information available for 1JI5)

(no "Cis Peptide Bond" information available for 1JI5)

(no "SAP(SNP)/Variant" information available for 1JI5)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DPS_1	PS00818	Dps protein family signature 1.	DPS2_BACAN	27-43	4	A:27-43 B:27-43 C:27-43 D:27-43
2	DPS_2	PS00819	Dps protein family signature 2.	DPS2_BACAN	53-67	4	A:53-67 B:53-67 C:53-67 D:53-67

Biological Unit 1 (2, 24)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DPS_1	PS00818	Dps protein family signature 1.	DPS2_BACAN	27-43	12	A:27-43 B:27-43 C:27-43 D:27-43
2	DPS_2	PS00819	Dps protein family signature 2.	DPS2_BACAN	53-67	12	A:53-67 B:53-67 C:53-67 D:53-67

(no "Exon" information available for 1JI5)

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:142
 aligned with DPS2_BACAN | Q8RPQ2 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:142
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143  
           DPS2_BACAN     4 QVIEVLNKQVADWSVLFTKLHNFHWYVKGPQFFTLHEKFEELYTESATHIDEIAERILAIGGKPVATMKEYLEISSIQEAAYGETAEGMVEAIMKDYEMMLVELKKGMEIAQNSDDEMTSDLLLGIYTELEKHAWMLRAFLN 145
               SCOP domains d1ji5a_ A: Dodecameric ferritin homolog                                                                                                        SCOP domains
               CATH domains 1ji5A00 A:4-145  [code=1.20.1260.10, no name defined]                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------DPS_1            ---------DPS_2          ------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ji5 A   4 QVIEVLNKQVADWSVLFTKLHNFHWYVKGPQFFTLHEKFEELYTESATHIDEIAERILAIGGKPVATMKEYLEISSIQEAAYGETAEGMVEAIMKDYEMMLVELKKGMEIAQNSDDEMTSDLLLGIYTELEKHAWMLRAFLN 145
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143

Chain B from PDB  Type:PROTEIN  Length:142
 aligned with DPS2_BACAN | Q8RPQ2 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:142
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143  
           DPS2_BACAN     4 QVIEVLNKQVADWSVLFTKLHNFHWYVKGPQFFTLHEKFEELYTESATHIDEIAERILAIGGKPVATMKEYLEISSIQEAAYGETAEGMVEAIMKDYEMMLVELKKGMEIAQNSDDEMTSDLLLGIYTELEKHAWMLRAFLN 145
               SCOP domains d1ji5b_ B: Dodecameric ferritin homolog                                                                                                        SCOP domains
               CATH domains 1ji5B00 B:4-145  [code=1.20.1260.10, no name defined]                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------DPS_1            ---------DPS_2          ------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ji5 B   4 QVIEVLNKQVADWSVLFTKLHNFHWYVKGPQFFTLHEKFEELYTESATHIDEIAERILAIGGKPVATMKEYLEISSIQEAAYGETAEGMVEAIMKDYEMMLVELKKGMEIAQNSDDEMTSDLLLGIYTELEKHAWMLRAFLN 145
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143

Chain C from PDB  Type:PROTEIN  Length:142
 aligned with DPS2_BACAN | Q8RPQ2 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:142
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143  
           DPS2_BACAN     4 QVIEVLNKQVADWSVLFTKLHNFHWYVKGPQFFTLHEKFEELYTESATHIDEIAERILAIGGKPVATMKEYLEISSIQEAAYGETAEGMVEAIMKDYEMMLVELKKGMEIAQNSDDEMTSDLLLGIYTELEKHAWMLRAFLN 145
               SCOP domains d1ji5c_ C: Dodecameric ferritin homolog                                                                                                        SCOP domains
               CATH domains 1ji5C00 C:4-145  [code=1.20.1260.10, no name defined]                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------DPS_1            ---------DPS_2          ------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ji5 C   4 QVIEVLNKQVADWSVLFTKLHNFHWYVKGPQFFTLHEKFEELYTESATHIDEIAERILAIGGKPVATMKEYLEISSIQEAAYGETAEGMVEAIMKDYEMMLVELKKGMEIAQNSDDEMTSDLLLGIYTELEKHAWMLRAFLN 145
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143

Chain D from PDB  Type:PROTEIN  Length:142
 aligned with DPS2_BACAN | Q8RPQ2 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:142
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143  
           DPS2_BACAN     4 QVIEVLNKQVADWSVLFTKLHNFHWYVKGPQFFTLHEKFEELYTESATHIDEIAERILAIGGKPVATMKEYLEISSIQEAAYGETAEGMVEAIMKDYEMMLVELKKGMEIAQNSDDEMTSDLLLGIYTELEKHAWMLRAFLN 145
               SCOP domains d1ji5d_ D: Dodecameric ferritin homolog                                                                                                        SCOP domains
               CATH domains 1ji5D00 D:4-145  [code=1.20.1260.10, no name defined]                                                                                          CATH domains
           Pfam domains (1) --Ferritin-1ji5D01 D:6-145                                                                                                                     Pfam domains (1)
           Pfam domains (2) --Ferritin-1ji5D02 D:6-145                                                                                                                     Pfam domains (2)
           Pfam domains (3) --Ferritin-1ji5D03 D:6-145                                                                                                                     Pfam domains (3)
           Pfam domains (4) --Ferritin-1ji5D04 D:6-145                                                                                                                     Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------DPS_1            ---------DPS_2          ------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ji5 D   4 QVIEVLNKQVADWSVLFTKLHNFHWYVKGPQFFTLHEKFEELYTESATHIDEIAERILAIGGKPVATMKEYLEISSIQEAAYGETAEGMVEAIMKDYEMMLVELKKGMEIAQNSDDEMTSDLLLGIYTELEKHAWMLRAFLN 145
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143

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)

Bacillus anthracis, Dlp-1 [TaxId: 1392] (1)

1a	d1ji5a_	A:
1b	d1ji5b_	B:
1c	d1ji5c_	C:
1d	d1ji5d_	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)

Bacillus anthracis. Organism_taxid: 1392. (2)

1a	1ji5A00	A:4-145
1b	1ji5B00	B:4-145
1c	1ji5C00	C:4-145
1d	1ji5D00	D:4-145

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ferritin (185)

Family: Ferritin (83)

Bacillus anthracis (3)

1a	Ferritin-1ji5D01	D:6-145
1b	Ferritin-1ji5D02	D:6-145
1c	Ferritin-1ji5D03	D:6-145
1d	Ferritin-1ji5D04	D:6-145

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (DPS2_BACAN | Q8RPQ2)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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.

Asymmetric Unit
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Biological Unit
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1ji4	1JI4 IS HP-NAP (NEUTROPHIL ACTIVATING PROTEIN)
1qgh	1QGH IS MINI-FERRITIN FROM LISTERIA INNOCUA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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