3ISF - JenaLib

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Asym. Unit - sites (Jmol Viewer)

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   STRUCTURE OF NON-MINERALIZED BFRB (AS-ISOLATED) FROM PSEUDOMONAS AERUGINOSA TO 2.07A RESOLUTION

Authors :   S. Lovell, S. K. Weeratunga, K. P. Battaile, M. Rivera

Date :   25 Aug 09 (Deposition) - 02 Feb 10 (Release) - 23 Feb 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.07

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

Keywords :   Electron Transport; Iron Storage, Heme, Iron, Iron Storage, Metal-Binding, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. K. Weeratunga, S. Lovell, H. Yao, K. P. Battaile, C. J. Fischer, C. E. Gee, M. Rivera
Structural Studies Of Bacterioferritin B From Pseudomonas Aeruginosa Suggest A Gating Mechanism For Iron Uptake Via The Ferroxidase Center
Biochemistry V. 49 1160 2010
PubMed-ID: 20067302 | Reference-DOI: 10.1021/BI9015204

Molecule 1 - BACTERIOFERRITIN
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	ARCTIC EXPRESS RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BFRB, PA3531
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	K	2	Ligand/Ion	POTASSIUM ION

Biological Unit 1 (1, 16)

No.	Name	Count	Type	Full Name
1	HEM	16	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	K	-1	Ligand/Ion	POTASSIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:148 , GLN A:151 , ASN D:148 , GLN D:151	BINDING SITE FOR RESIDUE K A 159
2	AC2	SOFTWARE	ASN A:23 , PHE A:26 , TYR A:45 , ILE A:49 , MET A:52 , LYS A:53 , LEU B:19 , ILE B:22 , ASN B:23 , PHE B:26 , TYR B:45 , ILE B:49 , MET B:52 , LYS B:53 , HOH B:355 , HOH B:360 , HOH B:361	BINDING SITE FOR RESIDUE HEM B 159
3	AC3	SOFTWARE	ASN B:148 , GLN B:151 , ASN C:148 , GLN C:151 , ASN E:148 , GLN E:151 , ASN F:148 , GLN F:151	BINDING SITE FOR RESIDUE K B 160
4	AC4	SOFTWARE	ILE C:22 , ASN C:23 , PHE C:26 , TYR C:45 , ILE C:49 , MET C:52 , LYS C:53 , HOH C:362 , HOH C:363 , ASN D:23 , PHE D:26 , TYR D:45 , ILE D:49 , MET D:52 , LYS D:53	BINDING SITE FOR RESIDUE HEM C 159
5	AC5	SOFTWARE	LEU E:19 , ILE E:22 , ASN E:23 , PHE E:26 , TYR E:45 , ILE E:49 , MET E:52 , LYS E:53 , HOH E:171	BINDING SITE FOR RESIDUE HEM E 159
6	AC6	SOFTWARE	LEU F:19 , ILE F:22 , ASN F:23 , PHE F:26 , TYR F:45 , ILE F:49 , MET F:52 , LYS F:53 , ALA F:55 , HOH F:189 , HOH F:359	BINDING SITE FOR RESIDUE HEM F 159

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

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

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

(no "PROSITE Motif" information available for 3ISF)

(no "Exon" information available for 3ISF)

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:155
 aligned with Q9HY79_PSEAE | Q9HY79 from UniProtKB/TrEMBL  Length:158

    Alignment length:155
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151     
         Q9HY79_PSEAE     2 KGDKKVIQHLNKILGNELIAINQYFLHSRMWNDWGLKRLGAHEYHESIDEMKHADKLIERILFLEGLPNLQDLGKLLIGENTQEMLQCDLNLELKATKDLREAIVHCEQVHDYVSRDLLKDILESEEEHIDYLETQLGLIQKVGLENYLQSHMHE 156
               SCOP domains d3isfa_ A: automated matches                                                                                                                                SCOP domains
               CATH domains 3isfA00 A:2-156  [code=1.20.1260.10, no name defined]                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3isf A   2 KGDKKVIQHLNKILGNELIAINQYFLHSRMWNDWGLKRLGAHEYHESIDEMKHADKLIERILFLEGLPNLQDLGKLLIGENTQEMLQCDLNLELKATKDLREAIVHCEQVHDYVSRDLLKDILESEEEHIDYLETQLGLIQKVGLENYLQSHMHE 156
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain B from PDB  Type:PROTEIN  Length:155
 aligned with Q9HY79_PSEAE | Q9HY79 from UniProtKB/TrEMBL  Length:158

    Alignment length:155
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151     
         Q9HY79_PSEAE     2 KGDKKVIQHLNKILGNELIAINQYFLHSRMWNDWGLKRLGAHEYHESIDEMKHADKLIERILFLEGLPNLQDLGKLLIGENTQEMLQCDLNLELKATKDLREAIVHCEQVHDYVSRDLLKDILESEEEHIDYLETQLGLIQKVGLENYLQSHMHE 156
               SCOP domains d3isfb_ B: automated matches                                                                                                                                SCOP domains
               CATH domains 3isfB00 B:2-156  [code=1.20.1260.10, no name defined]                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3isf B   2 KGDKKVIQHLNKILGNELIAINQYFLHSRMWNDWGLKRLGAHEYHESIDEMKHADKLIERILFLEGLPNLQDLGKLLIGENTQEMLQCDLNLELKATKDLREAIVHCEQVHDYVSRDLLKDILESEEEHIDYLETQLGLIQKVGLENYLQSHMHE 156
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain C from PDB  Type:PROTEIN  Length:156
 aligned with Q9HY79_PSEAE | Q9HY79 from UniProtKB/TrEMBL  Length:158

    Alignment length:156
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      
         Q9HY79_PSEAE     2 KGDKKVIQHLNKILGNELIAINQYFLHSRMWNDWGLKRLGAHEYHESIDEMKHADKLIERILFLEGLPNLQDLGKLLIGENTQEMLQCDLNLELKATKDLREAIVHCEQVHDYVSRDLLKDILESEEEHIDYLETQLGLIQKVGLENYLQSHMHED 157
               SCOP domains d3isfc_ C: automated matches                                                                                                                                 SCOP domains
               CATH domains 3isfC00 C:2-157  [code=1.20.1260.10, no name defined]                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3isf C   2 KGDKKVIQHLNKILGNELIAINQYFLHSRMWNDWGLKRLGAHEYHESIDEMKHADKLIERILFLEGLPNLQDLGKLLIGENTQEMLQCDLNLELKATKDLREAIVHCEQVHDYVSRDLLKDILESEEEHIDYLETQLGLIQKVGLENYLQSHMHED 157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain D from PDB  Type:PROTEIN  Length:157
 aligned with Q9HY79_PSEAE | Q9HY79 from UniProtKB/TrEMBL  Length:158

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
         Q9HY79_PSEAE     1 MKGDKKVIQHLNKILGNELIAINQYFLHSRMWNDWGLKRLGAHEYHESIDEMKHADKLIERILFLEGLPNLQDLGKLLIGENTQEMLQCDLNLELKATKDLREAIVHCEQVHDYVSRDLLKDILESEEEHIDYLETQLGLIQKVGLENYLQSHMHED 157
               SCOP domains d3isfd_ D: automated matches                                                                                                                                  SCOP domains
               CATH domains 3isfD00 D:1-157  [code=1.20.1260.10, no name defined]                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3isf D   1 MKGDKKVIQHLNKILGNELIAINQYFLHSRMWNDWGLKRLGAHEYHESIDEMKHADKLIERILFLEGLPNLQDLGKLLIGENTQEMLQCDLNLELKATKDLREAIVHCEQVHDYVSRDLLKDILESEEEHIDYLETQLGLIQKVGLENYLQSHMHED 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain E from PDB  Type:PROTEIN  Length:155
 aligned with Q9HY79_PSEAE | Q9HY79 from UniProtKB/TrEMBL  Length:158

    Alignment length:155
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151     
         Q9HY79_PSEAE     2 KGDKKVIQHLNKILGNELIAINQYFLHSRMWNDWGLKRLGAHEYHESIDEMKHADKLIERILFLEGLPNLQDLGKLLIGENTQEMLQCDLNLELKATKDLREAIVHCEQVHDYVSRDLLKDILESEEEHIDYLETQLGLIQKVGLENYLQSHMHE 156
               SCOP domains d3isfe_ E: automated matches                                                                                                                                SCOP domains
               CATH domains 3isfE00 E:2-156  [code=1.20.1260.10, no name defined]                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3isf E   2 KGDKKVIQHLNKILGNELIAINQYFLHSRMWNDWGLKRLGAHEYHESIDEMKHADKLIERILFLEGLPNLQDLGKLLIGENTQEMLQCDLNLELKATKDLREAIVHCEQVHDYVSRDLLKDILESEEEHIDYLETQLGLIQKVGLENYLQSHMHE 156
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain F from PDB  Type:PROTEIN  Length:155
 aligned with Q9HY79_PSEAE | Q9HY79 from UniProtKB/TrEMBL  Length:158

    Alignment length:155
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151     
         Q9HY79_PSEAE     2 KGDKKVIQHLNKILGNELIAINQYFLHSRMWNDWGLKRLGAHEYHESIDEMKHADKLIERILFLEGLPNLQDLGKLLIGENTQEMLQCDLNLELKATKDLREAIVHCEQVHDYVSRDLLKDILESEEEHIDYLETQLGLIQKVGLENYLQSHMHE 156
               SCOP domains d3isff_ F: automated matches                                                                                                                                SCOP domains
               CATH domains 3isfF00 F:2-156  [code=1.20.1260.10, no name defined]                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3isf F   2 KGDKKVIQHLNKILGNELIAINQYFLHSRMWNDWGLKRLGAHEYHESIDEMKHADKLIERILFLEGLPNLQDLGKLLIGENTQEMLQCDLNLELKATKDLREAIVHCEQVHDYVSRDLLKDILESEEEHIDYLETQLGLIQKVGLENYLQSHMHE 156
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

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: automated matches (70)

Pseudomonas aeruginosa [TaxId: 287] (5)

1a	d3isfa_	A:
1b	d3isfe_	E:
1c	d3isff_	F:
1d	d3isfb_	B:
1e	d3isfc_	C:
1f	d3isfd_	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)

Pseudomonas aeruginosa. Organism_taxid: 287. (4)

1a	3isfD00	D:1-157
1b	3isfC00	C:2-157
1c	3isfA00	A:2-156
1d	3isfB00	B:2-156
1e	3isfE00	E:2-156
1f	3isfF00	F:2-156

(no "Pfam Domain" information available for 3ISF)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (Q9HY79_PSEAE | Q9HY79)

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.
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.

Asymmetric Unit
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	Cis Peptide Bonds
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Biological Unit
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		Biological Unit 1	[ Jena3D ]

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	3isf
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Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (8, 8)

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