3R2H - JenaLib

Asymmetric Unit

Asym. Unit - sites

Biological Unit 1

Biol. Unit 1 - sites

collapse

expand

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Description

Title :   1.7 A RESOLUTION STRUCTURE OF AS-ISOLATED FTNA FROM PSEUDOMONAS AERUGINOSA (PH 10.5)

Authors :   S. W. Lovell, K. P. Battaile, H. Yao, G. Jepkorir, P. V. Nama, S. Weeratun M. Rivera

Date :   14 Mar 11 (Deposition) - 25 May 11 (Release) - 29 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A
Biol. Unit 1: A  (24x)

Keywords :   Bacterial Ferritin, Iron Binding, Iron Storage, Iron Homeostasis, Iron Release, Iron Mobilization, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Yao, G. Jepkorir, S. Lovell, P. V. Nama, S. Weeratunga, K. P. Battaile, M. Rivera
Two Distinct Ferritin-Like Molecules In Pseudomonas Aeruginosa: The Product Of The Bfra Gene Is A Bacterial Ferritin (Ftna) And Not A Bacterioferritin (Bfr).
Biochemistry V. 50 5236 2011
PubMed-ID: 21574546 | Reference-DOI: 10.1021/BI2004119

Compounds

Molecule 1 - BACTERIOFERRITIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3) GOLD
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	BFR, BFRA, PA4235
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287
	Strain	:	PAO1
	Synonym	:	BFR

Structural Features

Chains, Units

		1
Asymmetric Unit	:	A
Biological Unit 1 (24x)	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 4)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CXS	1	Ligand/Ion	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
2	NA	3	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 24)

No.	Name	Count	Type	Full Name
1	CXS	24	Ligand/Ion	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
2	NA	-1	Ligand/Ion	SODIUM ION

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:70 , ASP A:74 , HIS A:77 , LYS A:91 , HIS A:95 , HOH A:191 , HOH A:193 , HOH A:264 , HOH A:300	BINDING SITE FOR RESIDUE CXS A 155
2	AC2	SOFTWARE	GLU A:18 , GLU A:51 , HIS A:54 , NA A:157 , HOH A:304 , HOH A:307	BINDING SITE FOR RESIDUE NA A 156
3	AC3	SOFTWARE	GLU A:51 , GLU A:93 , NA A:156 , HOH A:281 , HOH A:303 , HOH A:307	BINDING SITE FOR RESIDUE NA A 157
4	AC4	SOFTWARE	ASN A:148 , GLN A:151	BINDING SITE FOR RESIDUE NA A 158

SS Bonds (0, 0)

(no "SS Bond" information available for 3R2H)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 3R2H)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 3R2H)

PROSITE Motifs (2, 2)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BACTERIOFERRITIN	PS00549	Bacterioferritin signature.	BFR_PSEAE	1-19	1	A:1-19
2	FERRITIN_LIKE	PS50905	Ferritin-like diiron domain profile.	BFR_PSEAE	1-145	1	A:1-145

Biological Unit 1 (2, 48)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BACTERIOFERRITIN	PS00549	Bacterioferritin signature.	BFR_PSEAE	1-19	24	A:1-19
2	FERRITIN_LIKE	PS50905	Ferritin-like diiron domain profile.	BFR_PSEAE	1-145	24	A:1-145

Exons (0, 0)

(no "Exon" information available for 3R2H)

Sequences/Alignments

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:154
 aligned with BFR_PSEAE | Q9HWF9 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    
            BFR_PSEAE     1 MQGHPEVIDYLNTLLTGELAARDQYFIHSRMYEDWGFSKLYERLNHEMEEETQHADALLRRILLLEGTPRMRPDDIHPGTTVPEMLEADLKLERHVRAALAKGIALCEQHKDFVSRDILKAQLADTEEDHAYWLEQQLGLIARMGLENYLQSQI 154
               SCOP domains d3r2ha_ A: automated matches                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------Ferritin-3r2hA01 A:8-144                                                                                                                 ---------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) BACTERIOFERRITIN   --------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) FERRITIN_LIKE  PDB: A:1-145 UniProt: 1-145                                                                                                       --------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r2h A   1 MQGHPEVIDYLNTLLTGELAARDQYFIHSRMYEDWGFSKLYERLNHEMEEETQHADALLRRILLLEGTPRMRPDDIHPGTTVPEMLEADLKLERHVRAALAKGIALCEQHKDFVSRDILKAQLADTEEDHAYWLEQQLGLIARMGLENYLQSQI 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

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)

Pseudomonas aeruginosa [TaxId: 287] (7)

d3r2ha_

CATH Domains (0, 0)

(no "CATH Domain" information available for 3R2H)

Pfam Domains (1, 1)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ferritin (185)

Family: Ferritin (83)

Pseudomonas aeruginosa (7)

Ferritin-3r2hA01

A:8-144

Gene Ontology (9, 9)

Asymmetric Unit(hide GO term definitions)

Chain A (BFR_PSEAE | Q9HWF9)

molecular function
	GO:0008199	ferric iron binding	Interacting selectively and non-covalently with ferric iron, Fe(III).
	GO:0004322	ferroxidase activity	Catalysis of the reaction: 4 Fe2+ + 4 H+ + O2 = 4 Fe3+ + 2 H2O.
	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:0006880	intracellular sequestering of iron ion	The process of binding or confining iron ions in an intracellular area such that they are separated from other components of a biological system.
	GO:0006826	iron ion transport	The directed movement of iron (Fe) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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.
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.

Visualization

Interactive Views

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
		CXS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ 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 3r2h)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

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)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3r2h
		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
	BFR_PSEAE \| Q9HWF9
		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

Analysis Tools

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
	BFR_PSEAE \| Q9HWF9
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	BFR_PSEAE \| Q9HWF9	:	3r2k 3r2l 3r2m 3r2o 3r2r 3r2s

Related Entries Specified in the PDB File

3r2k 3r2l 3r2m 3r2o 3r2r 3r2s