2CHP - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE DODECAMERIC FERRITIN MRGA FROM B. SUBTILIS 168

Authors :   L. -O. Essen, A. Morbitzer

Date :   16 Mar 06 (Deposition) - 03 Apr 07 (Release) - 05 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Dna-Binding Protein, Dps, Dodecameric, Ferritin, Dna-Binding, Stress Protein, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Schonafinger, A. Morbitzer, D. Kress, L. Essen, F. Noll, N. Hampp
Morphology Of Dry Solid-Supported Protein Monolayers Dependent On The Substrate And Protein Surface Properties.
Langmuir V. 22 7185 2006
PubMed-ID: 16893214 | Reference-DOI: 10.1021/LA0530182

Molecule 1 - METALLOREGULATION DNA-BINDING STRESS PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	GOLD
	Organism Scientific	:	BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168
	Organism Taxid	:	224308
	Synonym	:	MRGA

		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 (1, 2)

No.	Name	Count	Type	Full Name
1	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	PO4	6	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS B:42 , THR B:45 , HOH B:2029	BINDING SITE FOR RESIDUE PO4 B 1154
2	AC2	SOFTWARE	HIS A:42 , THR A:45 , HIS C:42 , THR C:45 , HIS D:42 , THR D:45	BINDING SITE FOR RESIDUE PO4 D 1154

(no "SS Bond" information available for 2CHP)

(no "Cis Peptide Bond" information available for 2CHP)

(no "SAP(SNP)/Variant" information available for 2CHP)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DPS_1	PS00818	Dps protein family signature 1.	MRGA_BACSU	35-51	4	A:35-51 B:35-51 C:35-51 D:35-51
2	DPS_2	PS00819	Dps protein family signature 2.	MRGA_BACSU	61-75	4	A:61-75 B:61-75 C:61-75 D:61-75

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.	MRGA_BACSU	35-51	12	A:35-51 B:35-51 C:35-51 D:35-51
2	DPS_2	PS00819	Dps protein family signature 2.	MRGA_BACSU	61-75	12	A:61-75 B:61-75 C:61-75 D:61-75

(no "Exon" information available for 2CHP)

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:148
 aligned with MRGA_BACSU | P37960 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:148
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145        
           MRGA_BACSU     6 AKTNQTLVENSLNTQLSNWFLLYSKLHRFHWYVKGPHFFTLHEKFEELYDHAAETVDTIAERLLAIGGQPVATVKEYTEHASITDGGNETSASEMVQALVNDYKQISSESKFVIGLAEENQDNATADLFVGLIEEVEKQVWMLSSYLG 153
               SCOP domains d2chpa_ A: automated matches                                                                                                                         SCOP domains
               CATH domains 2chpA00 A:6-153  [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 -----------------------------DPS_1            ---------DPS_2          ------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2chp A   6 AKTNQTLVENSLNTQLSNWFLLYSKLHRFHWYVKGPHFFTLHEKFEELYDHAAETVDTIAERLLAIGGQPVATVKEYTEHASITDGGNETSASEMVQALVNDYKQISSESKFVIGLAEENQDNATADLFVGLIEEVEKQVWMLSSYLG 153
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145

Chain B from PDB  Type:PROTEIN  Length:147
 aligned with MRGA_BACSU | P37960 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:147
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       
           MRGA_BACSU     7 KTNQTLVENSLNTQLSNWFLLYSKLHRFHWYVKGPHFFTLHEKFEELYDHAAETVDTIAERLLAIGGQPVATVKEYTEHASITDGGNETSASEMVQALVNDYKQISSESKFVIGLAEENQDNATADLFVGLIEEVEKQVWMLSSYLG 153
               SCOP domains d2chpb_ B: automated matches                                                                                                                        SCOP domains
               CATH domains 2chpB00 B:7-153  [code=1.20.1260.10, no name defined]                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------DPS_1            ---------DPS_2          ------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2chp B   7 KTNQTLVENSLNTQLSNWFLLYSKLHRFHWYVKGPHFFTLHEKFEELYDHAAETVDTIAERLLAIGGQPVATVKEYTEHASITDGGNETSASEMVQALVNDYKQISSESKFVIGLAEENQDNATADLFVGLIEEVEKQVWMLSSYLG 153
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146

Chain C from PDB  Type:PROTEIN  Length:145
 aligned with MRGA_BACSU | P37960 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:145
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148     
           MRGA_BACSU     9 NQTLVENSLNTQLSNWFLLYSKLHRFHWYVKGPHFFTLHEKFEELYDHAAETVDTIAERLLAIGGQPVATVKEYTEHASITDGGNETSASEMVQALVNDYKQISSESKFVIGLAEENQDNATADLFVGLIEEVEKQVWMLSSYLG 153
               SCOP domains d2chpc_ C: automated matches                                                                                                                      SCOP domains
               CATH domains 2chpC00 C:9-153  [code=1.20.1260.10, no name defined]                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------DPS_1            ---------DPS_2          ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2chp C   9 NQTLVENSLNTQLSNWFLLYSKLHRFHWYVKGPHFFTLHEKFEELYDHAAETVDTIAERLLAIGGQPVATVKEYTEHASITDGGNETSASEMVQALVNDYKQISSESKFVIGLAEENQDNATADLFVGLIEEVEKQVWMLSSYLG 153
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148

Chain D from PDB  Type:PROTEIN  Length:145
 aligned with MRGA_BACSU | P37960 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:145
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148     
           MRGA_BACSU     9 NQTLVENSLNTQLSNWFLLYSKLHRFHWYVKGPHFFTLHEKFEELYDHAAETVDTIAERLLAIGGQPVATVKEYTEHASITDGGNETSASEMVQALVNDYKQISSESKFVIGLAEENQDNATADLFVGLIEEVEKQVWMLSSYLG 153
               SCOP domains d2chpd_ D: automated matches                                                                                                                      SCOP domains
               CATH domains 2chpD00 D:9-153  [code=1.20.1260.10, no name defined]                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------DPS_1            ---------DPS_2          ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2chp D   9 NQTLVENSLNTQLSNWFLLYSKLHRFHWYVKGPHFFTLHEKFEELYDHAAETVDTIAERLLAIGGQPVATVKEYTEHASITDGGNETSASEMVQALVNDYKQISSESKFVIGLAEENQDNATADLFVGLIEEVEKQVWMLSSYLG 153
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148

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: automated matches (54)

Protein domain: automated matches (54)

Bacillus subtilis [TaxId: 1423] (2)

1a	d2chpa_	A:
1b	d2chpb_	B:
1c	d2chpc_	C:
1d	d2chpd_	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 subtilis. Organism_taxid: 1423. Strain: 168. (1)

1a	2chpA00	A:6-153
1b	2chpB00	B:7-153
1c	2chpC00	C:9-153
1d	2chpD00	D:9-153

(no "Pfam Domain" information available for 2CHP)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (MRGA_BACSU | P37960)

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: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: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.

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
		PO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2chp)

Biological Unit
	Complete Structure
		Biological Unit 1	[ 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 ](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
	2chp
		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
	MRGA_BACSU \| P37960
		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
	MRGA_BACSU \| P37960
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 2CHP)

(no "Related Entries Specified in the PDB File" available for 2CHP)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

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 (0, 0)

Gene Ontology (7, 7)

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