2WHY - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE TRISCATECHOLATE SIDEROPHORE BINDING PROTEIN FEUA FROM BACILLUS SUBTILIS COMPLEXED WITH FERRI-BACILLIBACTIN

Authors :   F. Peuckert, M. Miethke, A. G. Albrecht, L. -O. Essen, M. A. Marahiel

Date :   07 May 09 (Deposition) - 29 Sep 09 (Release) - 28 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Transport Protein, Bacillibactin And Enterobactin Binding, Triscatecholate Binding Protein, Iron Transport, High Affinity Iron Import, Iron, Membrane, Palmitate, Transport, Abc-Type Transporter Binding Protein, Siderophore Binding Protein, Lipoprotein, Cell Membrane, Ion Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Peuckert, M. Miethke, A. G. Albrecht, L. -O. Essen, M. A. Marahiel
Structural Basis And Stereochemistry Of Triscatecholate Siderophore Binding By Feua.
Angew. Chem. Int. Ed. Engl. V. 48 7924 2009
PubMed-ID: 19746494 | Reference-DOI: 10.1002/ANIE.200902495

Molecule 1 - IRON-UPTAKE SYSTEM-BINDING PROTEIN
	Atcc	:	21332
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	POK01
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PCB-28A
	Fragment	:	RESIDUES 21-317
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

Molecule 2 - BACILLIBACTIN
	Chains	:	B
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	CORYNEBACTIN, 9-GLN-BETA-LIPOTROPIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 15)

No.	Name	Count	Type	Full Name
1	CL	11	Ligand/Ion	CHLORIDE ION
2	DBH	3	Mod. Amino Acid	2,3-DIHYDROXY-BENZOIC ACID
3	FE	1	Ligand/Ion	FE (III) ION

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	DBH	3	Mod. Amino Acid	2,3-DIHYDROXY-BENZOIC ACID
3	FE	-1	Ligand/Ion	FE (III) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	DBH	-1	Mod. Amino Acid	2,3-DIHYDROXY-BENZOIC ACID
3	FE	-1	Ligand/Ion	FE (III) ION

Biological Unit 3 (1, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	DBH	3	Mod. Amino Acid	2,3-DIHYDROXY-BENZOIC ACID
3	FE	-1	Ligand/Ion	FE (III) ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:173 , GLU A:208	BINDING SITE FOR RESIDUE CL A1302
2	AC2	SOFTWARE	THR A:120	BINDING SITE FOR RESIDUE CL A1303
3	AC3	SOFTWARE	ASP A:237 , HOH A:2104	BINDING SITE FOR RESIDUE CL A1304
4	AC4	SOFTWARE	TRP A:130 , ASP A:200 , HOH A:2082 , HOH A:2132	BINDING SITE FOR RESIDUE CL A1305
5	AC5	SOFTWARE	ASP A:153 , ASP A:157 , HOH A:2067	BINDING SITE FOR RESIDUE CL A1306
6	AC6	SOFTWARE	SER A:219 , LEU A:220 , GLU A:221	BINDING SITE FOR RESIDUE CL A1307
7	AC7	SOFTWARE	HOH A:2124	BINDING SITE FOR RESIDUE CL A1310
8	AC8	SOFTWARE	DBH B:11 , DBH B:21 , DBH B:31	BINDING SITE FOR RESIDUE FE B1001
9	KKR	AUTHOR	LYS A:84 , LYS A:105 , ARG A:180	MAIN MOTIF RESPONSIBLE FOR BINDING OF TRISCATECHOLATES

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

Asymmetric Unit

No.	Residues
1	Val A:33	-	Pro A:34

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FE_B12_PBP	PS50983	Iron siderophore/cobalamin periplasmic-binding domain profile.	FEUA_BACSU	57-317	1	A:38-298

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FE_B12_PBP	PS50983	Iron siderophore/cobalamin periplasmic-binding domain profile.	FEUA_BACSU	57-317	1	A:38-298

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FE_B12_PBP	PS50983	Iron siderophore/cobalamin periplasmic-binding domain profile.	FEUA_BACSU	57-317	1	A:38-298

Biological Unit 3 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FE_B12_PBP	PS50983	Iron siderophore/cobalamin periplasmic-binding domain profile.	FEUA_BACSU	57-317	0	-

(no "Exon" information available for 2WHY)

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
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Chain A from PDB  Type:PROTEIN  Length:283
 aligned with FEUA_BACSU | P40409 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:283
                                                                                                                                                                                                                                                                                                                 317   
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317   
           FEUA_BACSU    38 KKKIEYLDKTYEVTVPTDKIAITGSVESMEDAKLLDVHPQGAISFSGKFPDMFKDITDKAEPTGEKMEPNIEKILEMKPDVILASTKFPEKTLQKISTAGTTIPVSHISSNWKENMMLLAQLTGKEKKAKKIIADYEQDLKEIKTKINDKAKDSKALVIRIRQGNIYIYPEQVYFNSTLYGDLGLKAPNEVKAAKAQELSSLEKLSEMNPDHIFVQFSDDENADKPDALKDLEKNPIWKSLKAVKEDHVYVNSVDPLAQGGTAWSKVRFLKAAAEKLTQN---   -
               SCOP domains d2whya_ A: automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2whyA01 A:19-142 Nitrogenase molybdenum iron protein domain                                                                 2whyA02 A:143-301 Nitrogenase molybdenum iron protein domain                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeee......eee..hhhhhhhhhhhh....eeee.....hhhhh......eeeee....hhhhhhhhh..eeeee...hhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..eeee......hhhhhh.......hhhhhh.......hhhhhhhhh..eeeeee.hhhhh...hhhhhhhhh.hhhhhhhhhhh.eee..........hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------FE_B12_PBP  PDB: A:38-298 UniProt: 57-317                                                                                                                                                                                                                            --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2why A  19 KKKIEYLDKTYEVTVPTDKIAITGSVESMEDAKLLDVHPQGAISFSGKFPDMFKDITDKAEPTGEKMEPNIEKILEMKPDVILASTKFPEKTLQKISTAGTTIPVSHISSNWKENMMLLAQLTGKEKKAKKIIADYEQDLKETKTKINDKAKDSKALVIRIRQGNIYIYPEQVYFNSTLYGDLGLKAPNEVKAAKAQELISLEKLSEMNPDHIFVQFSDDENADKPDALKDLEKNPIWKSLKAVKEDHVYVNSVDPLAQGGTAWSKVRFLKAAAEKLTQNKLA 301
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298

Chain B from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 2why B  11 xGTxGTxGT  33
                            | || ||  
                           11-DBH||  
                             13| ||  
                              21-DBH 
                                23|  
                                 31-DBH

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Chelatase-like (149)

Superfamily: Helical backbone metal receptor (102)

Family: TM0189-like (10)

Protein domain: automated matches (5)

Bacillus subtilis [TaxId: 1423] (4)

d2whya_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Nitrogenase molybdenum iron protein domain (45)

Bacillus subtilis. Organism_taxid: 1423. (2)

1a	2whyA01	A:19-142
1b	2whyA02	A:143-301

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

Asymmetric Unit(hide GO term definitions)

Chain A (FEUA_BACSU | P40409)

biological process
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0055072	iron ion homeostasis	Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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		Val A:33 - Pro A:34	[ RasMol ]

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	2why
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	FEUA_BACSU \| P40409	:	2phz 2wi8 2xuz 2xv1

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 15)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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