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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF BORDETELLA PERTUSSIS HOLO FERRIC BINDING PROTEIN BOUND WITH TWO SYNERGISTIC OXALATE ANIONS

Authors :   S. A. L. Tom-Yew, M. E. P. Murphy

Date :   16 Feb 07 (Deposition) - 26 Feb 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.49

Chains :   Asym./Biol. Unit : A

Keywords :   Alpha-Beta-Alpha Units, Anti-Parallel Beta-Strands Hinge Region, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. A. L. Tom-Yew, B. H. Shilton, E. G. Bekker, E. I. Tocheva, M. E. P. Murphy
Anion-Dependent Hinge Motion In Ferric Binding Proteins
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PUTATIVE IRON BINDING PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	BFBPA
	Organism Scientific	:	BORDETELLA PERTUSSIS TOHAMA I
	Organism Taxid	:	257313
	Strain	:	TOHAMA I

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	FE	1	Ligand/Ion	FE (III) ION
2	OXL	2	Ligand/Ion	OXALATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:143 , TYR A:200	BINDING SITE FOR RESIDUE FE A 324
2	AC2	SOFTWARE	ARG A:137 , TYR A:143 , GLY A:178 , ASP A:179 , ARG A:180 , TYR A:200 , HOH A:339 , HOH A:519	BINDING SITE FOR RESIDUE OXL A 325
3	AC3	SOFTWARE	ARG A:14 , TYR A:143 , TYR A:200 , HOH A:384 , HOH A:501 , HOH A:546	BINDING SITE FOR RESIDUE OXL A 326

Asymmetric/Biological Unit

No.	Residues
1	A:135	-	A:191

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

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

(no "PROSITE Motif" information available for 2OWS)

(no "Exon" information available for 2OWS)

Asymmetric/Biological 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:314
 aligned with Q7VXW9_BORPE | Q7VXW9 from UniProtKB/TrEMBL  Length:349

    Alignment length:318
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341        
         Q7VXW9_BORPE    32 DEVSLYTTREPKLIQPLLDAFAKDSGIKVNTVFVKDGLLERVRAEGDKSPADVLMTVDIGNLIDLVNGGVTQKIQSQTLDSVVPANLRGAEGSWYALSLRDRVLYVEKDLKLDSFRYGDLADPKWKGKVCIRSGQHPYNTALVAAMIAHDGAEATEKWLRGVKANLARKAAGGDRDVARDILGGICDIGLANAYYVGHMKNAEPGTDARKWGDAIKVVRPTFATAKDGGTHVNISGAAVAAHAPNKANAVKLLEYLVSEPAQTLYAQANYEYPVRAGVKLDAVVASFGPLKVDTLPVAEIAKYRKQASELVDKVGFDN 349
               SCOP domains d2owsa_ A: automated matches                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2owsA01 A:6-102,A:234-283 Periplasmic binding protein-like II                                    2owsA02 A:103-233,A:284-323 Periplasmic binding protein-like II                                                                    2owsA01 A:6-102,A:234-283                         2owsA02 A:103-233,A:284-323              CATH domains
               Pfam domains -----------------------------------------------SBP_bac_6-2owsA01 A:53-298                                                                                                                                                                                                                            ------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhh...eeeeehhhhhhhhhhh..ee...hhhhhhhhhhhhhhhhhh.eeeeeeeeeeeee........hhhhhhhhhhh..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh....eeeeehhhhhhhhh....hhhhhhhhheeee.....----....eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhh..ee.......hhhhhhh.........hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ows A   6 DEVSLYTTREPKLIQPLLDAFAKDSGIKVNTVFVKDGLLERVRAEGDKSPADVLMTVDIGNLIDLVNGGVTQKIQSQTLDSVVPANLRGAEGSWYALSLRDRVLYVEKDLKLDSFRYGDLADPKWKGKVCIRSGQHPYNTALVAAMIAHDGAEATEKWLRGVKANLARKAAGGDRDVARDILGGICDIGLANAYYVGHMKNAEPGTDARKWGDAIKVVRPTFA----GGTHVNISGAAVAAHAPNKANAVKLLEYLVSEPAQTLYAQANYEYPVRAGVKLDAVVASFGPLKVDTLPVAEIAKYRKQASELVDKVGFDN 323
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225  |    235       245       255       265       275       285       295       305       315        
                                                                                                                                                                                                                                                        228  233

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Periplasmic binding protein-like II (813)

Superfamily: Periplasmic binding protein-like II (813)

Family: Phosphate binding protein-like (463)

Protein domain: automated matches (76)

Bordetella pertussis [TaxId: 257313] (2)

d2owsa_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: D-Maltodextrin-Binding Protein; domain 2 (600)

Homologous Superfamily: Periplasmic binding protein-like II (486)

Bordetella pertussis tohama i. Organism_taxid: 257313. Strain: tohamai. (2)

1a	2owsA01	A:6-102,A:234-283
1b	2owsA02	A:103-233,A:284-323

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PBP (391)

Family: SBP_bac_6 (7)

Bordetella pertussis (2)

SBP_bac_6-2owsA01

A:53-298

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q7VXW9_BORPE | Q7VXW9)

molecular function
	GO:0046872		metal ion binding		Interacting selectively and non-covalently with any metal ion.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ows)

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	2ows
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	Q7VXW9_BORPE \| Q7VXW9	:	1y9u 2owt

1y9u	APO FORM OF SAME PROTEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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