1N1Q - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A DPS PROTEIN FROM BACILLUS BREVIS

Authors :   B. Ren, G. Tibbelin, T. Kajino, O. Asami, R. Ladenstein

Date :   19 Oct 02 (Deposition) - 27 May 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: A,B,C,D  (3x)
Biol. Unit 3: C,D  (1x)
Biol. Unit 4: A,B  (1x)

Keywords :   Four-Helix Bundle, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Ren, G. Tibbelin, T. Kajino, O. Asami, R. Ladenstein
The Multi-Layered Structure Of Dps With A Novel Di-Nuclear Ferroxidase Center
J. Mol. Biol. V. 329 467 2003
PubMed-ID: 12767829 | Reference-DOI: 10.1016/S0022-2836(03)00466-2

Molecule 1 - DPS PROTEIN
	Chains	:	A, B, C, D
	Organism Scientific	:	BREVIBACILLUS BREVIS
	Organism Taxid	:	1393

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	FEO	4	Ligand/Ion	MU-OXO-DIIRON

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	FEO	4	Ligand/Ion	MU-OXO-DIIRON

Biological Unit 2 (1, 12)

No.	Name	Count	Type	Full Name
1	FEO	12	Ligand/Ion	MU-OXO-DIIRON

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	FEO	2	Ligand/Ion	MU-OXO-DIIRON

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	FEO	2	Ligand/Ion	MU-OXO-DIIRON

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:31 , HIS A:43 , HOH A:640 , HOH A:641 , ASP B:58 , GLU B:62	BINDING SITE FOR RESIDUE FEO B 515
2	AC2	SOFTWARE	ASP A:58 , GLU A:62 , LYS A:139 , HIS B:31 , HOH B:611 , HOH B:612	BINDING SITE FOR RESIDUE FEO A 516
3	AC3	SOFTWARE	HIS C:31 , LYS C:139 , HOH C:657 , HOH C:658 , ASP D:58 , GLU D:62	BINDING SITE FOR RESIDUE FEO D 517
4	AC4	SOFTWARE	ASP C:58 , GLU C:62 , HIS D:31 , HOH D:633 , HOH D:634	BINDING SITE FOR RESIDUE FEO C 518

(no "SS Bond" information available for 1N1Q)

(no "Cis Peptide Bond" information available for 1N1Q)

(no "SAP(SNP)/Variant" information available for 1N1Q)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DPS_1	PS00818	Dps protein family signature 1.	DPS_BREBE	31-47	4	A:31-47 B:31-47 C:31-47 D:31-47
2	DPS_2	PS00819	Dps protein family signature 2.	DPS_BREBE	57-71	4	A:57-71 B:57-71 C:57-71 D:57-71

Biological Unit 1 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DPS_1	PS00818	Dps protein family signature 1.	DPS_BREBE	31-47	4	A:31-47 B:31-47 C:31-47 D:31-47
2	DPS_2	PS00819	Dps protein family signature 2.	DPS_BREBE	57-71	4	A:57-71 B:57-71 C:57-71 D:57-71

Biological Unit 2 (2, 24)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DPS_1	PS00818	Dps protein family signature 1.	DPS_BREBE	31-47	12	A:31-47 B:31-47 C:31-47 D:31-47
2	DPS_2	PS00819	Dps protein family signature 2.	DPS_BREBE	57-71	12	A:57-71 B:57-71 C:57-71 D:57-71

Biological Unit 3 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DPS_1	PS00818	Dps protein family signature 1.	DPS_BREBE	31-47	2	- - C:31-47 D:31-47
2	DPS_2	PS00819	Dps protein family signature 2.	DPS_BREBE	57-71	2	- - C:57-71 D:57-71

Biological Unit 4 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DPS_1	PS00818	Dps protein family signature 1.	DPS_BREBE	31-47	2	A:31-47 B:31-47 - -
2	DPS_2	PS00819	Dps protein family signature 2.	DPS_BREBE	57-71	2	A:57-71 B:57-71 - -

(no "Exon" information available for 1N1Q)

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:149
 aligned with DPS_BREBE | P83695 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         
            DPS_BREBE     1 MKTSIQQLVAVLLNRQVANWVVLYVKLHNFHWNVNGPNFFTLHEKFEELYTEASGHIDTLAERVLSIGGSPIATLAASLEEASIKEATGGESAAEMVSSVVNDFVDLVGELKVARDVADEADDEATADMLDAIEAGLEKHVWMLEAFLE 149
               SCOP domains d1n1qa_ A: Dodecameric ferritin homolog                                                                                                               SCOP domains
               CATH domains 1n1qA00 A:1-149  [code=1.20.1260.10, no name defined]                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------DPS_1            ---------DPS_2          ------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n1q A   1 MKTSIQQLVAVLLNRQVANWVVLYVKLHNFHWNVNGPNFFTLHEKFEELYTEASGHIDTLAERVLSIGGSPIATLAASLEEASIKEATGGESAAEMVSSVVNDFVDLVGELKVARDVADEADDEATADMLDAIEAGLEKHVWMLEAFLE 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain B from PDB  Type:PROTEIN  Length:149
 aligned with DPS_BREBE | P83695 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         
            DPS_BREBE     1 MKTSIQQLVAVLLNRQVANWVVLYVKLHNFHWNVNGPNFFTLHEKFEELYTEASGHIDTLAERVLSIGGSPIATLAASLEEASIKEATGGESAAEMVSSVVNDFVDLVGELKVARDVADEADDEATADMLDAIEAGLEKHVWMLEAFLE 149
               SCOP domains d1n1qb_ B: Dodecameric ferritin homolog                                                                                                               SCOP domains
               CATH domains 1n1qB00 B:1-149  [code=1.20.1260.10, no name defined]                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------DPS_1            ---------DPS_2          ------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n1q B   1 MKTSIQQLVAVLLNRQVANWVVLYVKLHNFHWNVNGPNFFTLHEKFEELYTEASGHIDTLAERVLSIGGSPIATLAASLEEASIKEATGGESAAEMVSSVVNDFVDLVGELKVARDVADEADDEATADMLDAIEAGLEKHVWMLEAFLE 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain C from PDB  Type:PROTEIN  Length:146
 aligned with DPS_BREBE | P83695 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:146
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143      
            DPS_BREBE     4 SIQQLVAVLLNRQVANWVVLYVKLHNFHWNVNGPNFFTLHEKFEELYTEASGHIDTLAERVLSIGGSPIATLAASLEEASIKEATGGESAAEMVSSVVNDFVDLVGELKVARDVADEADDEATADMLDAIEAGLEKHVWMLEAFLE 149
               SCOP domains d1n1qc_ C: Dodecameric ferritin homolog                                                                                                            SCOP domains
               CATH domains 1n1qC00 C:4-149  [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
                 1n1q C   4 SIQQLVAVLLNRQVANWVVLYVKLHNFHWNVNGPNFFTLHEKFEELYTEASGHIDTLAERVLSIGGSPIATLAASLEEASIKEATGGESAAEMVSSVVNDFVDLVGELKVARDVADEADDEATADMLDAIEAGLEKHVWMLEAFLE 149
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143

Chain D from PDB  Type:PROTEIN  Length:144
 aligned with DPS_BREBE | P83695 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:144
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145    
            DPS_BREBE     6 QQLVAVLLNRQVANWVVLYVKLHNFHWNVNGPNFFTLHEKFEELYTEASGHIDTLAERVLSIGGSPIATLAASLEEASIKEATGGESAAEMVSSVVNDFVDLVGELKVARDVADEADDEATADMLDAIEAGLEKHVWMLEAFLE 149
               SCOP domains d1n1qd_ D: Dodecameric ferritin homolog                                                                                                          SCOP domains
               CATH domains 1n1qD00 D:6-149  [code=1.20.1260.10, no name defined]                                                                                            CATH domains
           Pfam domains (1) ----Ferritin-1n1qD01 D:10-149                                                                                                                    Pfam domains (1)
           Pfam domains (2) ----Ferritin-1n1qD02 D:10-149                                                                                                                    Pfam domains (2)
           Pfam domains (3) ----Ferritin-1n1qD03 D:10-149                                                                                                                    Pfam domains (3)
           Pfam domains (4) ----Ferritin-1n1qD04 D:10-149                                                                                                                    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
                 1n1q D   6 QQLVAVLLNRQVANWVVLYVKLHNFHWNVNGPNFFTLHEKFEELYTEASGHIDTLAERVLSIGGSPIATLAASLEEASIKEATGGESAAEMVSSVVNDFVDLVGELKVARDVADEADDEATADMLDAIEAGLEKHVWMLEAFLE 149
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145

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 brevis, Dps [TaxId: 1393] (1)

1a	d1n1qa_	A:
1b	d1n1qb_	B:
1c	d1n1qc_	C:
1d	d1n1qd_	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)

Brevibacillus brevis. Organism_taxid: 1393 (1)

1a	1n1qA00	A:1-149
1b	1n1qB00	B:1-149
1c	1n1qC00	C:4-149
1d	1n1qD00	D:6-149

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ferritin (185)

Family: Ferritin (83)

Brevibacillus brevis (Bacillus brevis) (1)

1a	Ferritin-1n1qD01	D:10-149
1b	Ferritin-1n1qD02	D:10-149
1c	Ferritin-1n1qD03	D:10-149
1d	Ferritin-1n1qD04	D:10-149

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (DPS_BREBE | P83695)

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:0030261	chromosome condensation	The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells.
	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.
	GO:0009295	nucleoid	The region of a virus, bacterial cell, mitochondrion or chloroplast to which the nucleic acid is confined.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		FEO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1n1q)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format \| Biol. Unit 4 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1n1q
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	DPS_BREBE \| P83695
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	DPS_BREBE \| P83695
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1N1Q)

(no "Related Entries Specified in the PDB File" available for 1N1Q)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 8)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (1, 4)

Gene Ontology (11, 11)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File