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Title :   CRYSTAL STRUCTURE OF PETROBACTIN-BINDING PROTEIN YCLQ FROM BACILLU SUBTILIS

Authors :   Y. Kim, N. Maltseva, A. M. Zawadzka, K. N. Raymond, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)

Date :   27 Feb 09 (Deposition) - 12 May 09 (Release) - 09 Feb 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Alpha-Beta-Sandwich, Periplasmic Binding Protein Fold (Pbp Fold), Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Secreted, Transport, Unknown Function, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. M. Zawadzka, Y. Kim, N. Maltseva, R. Nichiporuk, Y. Fan, A. Joachimiak, K. N. Raymond
Characterization Of A Bacillus Subtilis Transporter For Petrobactin, An Anthrax Stealth Siderophore.
Proc. Natl. Acad. Sci. Usa V. 106 21854 2009
PubMed-ID: 19955416 | Reference-DOI: 10.1073/PNAS.0904793106

Molecule 1 - UNCHARACTERIZED ABC TRANSPORTER SOLUTE-BINDING PROTEIN YCLQ
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21MAGIC
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 21-317
	Gene	:	BSU03830, YCLQ
	Organism Scientific	:	BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168
	Organism Taxid	:	224308
	Strain	:	SUBSP. SUBTILIS STR. 168

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	ASN	1	Mod. Amino Acid	ASPARAGINE
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	ASN	-1	Mod. Amino Acid	ASPARAGINE
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	ASN	1	Mod. Amino Acid	ASPARAGINE
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	-1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS B:265 , GLU B:298 , HOH B:380	BINDING SITE FOR RESIDUE ASN B 304
2	AC2	SOFTWARE	LYS A:84 , ARG A:104 , ARG A:192 , HIS A:214 , TYR A:275 , HOH A:409	BINDING SITE FOR RESIDUE PO4 A 304

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FE_B12_PBP	PS50983	Iron siderophore/cobalamin periplasmic-binding domain profile.	YCLQ_BACSU	56-317	2	A:36-297 B:36-297

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.	YCLQ_BACSU	56-317	1	A:36-297 -

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.	YCLQ_BACSU	56-317	1	- B:36-297

(no "Exon" information available for 3GFV)

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:286
 aligned with YCLQ_BACSU | P94421 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:286
                                                                                                                                                                                                                                                                                                                     317  
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313   |  
           YCLQ_BACSU    34 KEQITVKHQLDKNGTKVPKNPKKVVVFDFGSLDTLDKLGLDDIVAGLPKQVLPKYLSKFKDDKYADVGSLKEPDFDKVAELDPDLIIISARQSESYKEFSKIAPTIYLGVDTAKYMESFKSDAETIGKIFDKEDKVKDELANIDHSIADVKKTAEKLNKNGLVIMANDGKISAFGPKSRYGLIHDVFGVAPADQNIKASTHGQSVSYEYISKTNPDYLFVIDRGTAIGETSSTKQVVENDYVKNVNAVKNGHVIYLDSATWYLSGGGLESMTQMIKEVKDGLEK--   -
               SCOP domains d3gfva_ A: automated matches                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..eeeeeeee.....eee.hhhhhhhhhhh.hhh.eeee.....hhhhhhhhh...ee.......hhhhhhhh...eeeehhhhhhhhhhhhhhh.eee...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..eeeee......hhhhhh...ee...........eeehhhhhhhhh..eeeeeehhhhhh...hhhhhhhhhhhh.hhhhhh..eee.hhhhhhhh..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------FE_B12_PBP  PDB: A:36-297 UniProt: 56-317                                                                                                                                                                                                                             -- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gfv A  14 KEQITVKHQLDKNGTKVPKNPKKVVVFDFGSLDTLDKLGLDDIVAGLPKQVLPKYLSKFKDDKYADVGSLKEPDFDKVAELDPDLIIISARQSESYKEFSKIAPTIYLGVDTAKYmESFKSDAETIGKIFDKEDKVKDELANIDHSIADVKKTAEKLNKNGLVImANDGKISAFGPKSRYGLIHDVFGVAPADQNIKASTHGQSVSYEYISKTNPDYLFVIDRGTAIGETSSTKQVVENDYVKNVNAVKNGHVIYLDSATWYLSGGGLESmTQmIKEVKDGLEKEN 299
                                    23        33        43        53        63        73        83        93       103       113       123     | 133       143       153       163       173    |  183       193       203       213       223       233       243       253       263       273       283|  |   293      
                                                                                                                                             129-MSE                                          178-MSE                                                                                                   284-MSE           
                                                                                                                                                                                                                                                                                                           287-MSE

Chain B from PDB  Type:PROTEIN  Length:286
 aligned with YCLQ_BACSU | P94421 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:286
                                                                                                                                                                                                                                                                                                                     317  
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313   |  
           YCLQ_BACSU    34 KEQITVKHQLDKNGTKVPKNPKKVVVFDFGSLDTLDKLGLDDIVAGLPKQVLPKYLSKFKDDKYADVGSLKEPDFDKVAELDPDLIIISARQSESYKEFSKIAPTIYLGVDTAKYMESFKSDAETIGKIFDKEDKVKDELANIDHSIADVKKTAEKLNKNGLVIMANDGKISAFGPKSRYGLIHDVFGVAPADQNIKASTHGQSVSYEYISKTNPDYLFVIDRGTAIGETSSTKQVVENDYVKNVNAVKNGHVIYLDSATWYLSGGGLESMTQMIKEVKDGLEK--   -
               SCOP domains d3gfvb_ B: automated matches                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..eeeeeeee.....eee.hhhhhhhhhhh.hhh.eeee.....hhhhhhhhh...ee.......hhhhhhhh...eeeehhhhhhhhhhhhhhh.eee...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..eeeee......hhhhhh...ee...........eeehhhhhhhhh..eeeeeehhhhhh...hhhhhhhh.....hhhhhh..eee.hhhhhhhh..hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------FE_B12_PBP  PDB: B:36-297 UniProt: 56-317                                                                                                                                                                                                                             -- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gfv B  14 KEQITVKHQLDKNGTKVPKNPKKVVVFDFGSLDTLDKLGLDDIVAGLPKQVLPKYLSKFKDDKYADVGSLKEPDFDKVAELDPDLIIISARQSESYKEFSKIAPTIYLGVDTAKYmESFKSDAETIGKIFDKEDKVKDELANIDHSIADVKKTAEKLNKNGLVImANDGKISAFGPKSRYGLIHDVFGVAPADQNIKASTHGQSVSYEYISKTNPDYLFVIDRGTAIGETSSTKQVVENDYVKNVNAVKNGHVIYLDSATWYLSGGGLESmTQmIKEVKDGLEKEN 304
                                    23        33        43        53        63        73        83        93       103       113       123     | 133       143       153       163       173    |  183       193       203       213       223       233       243       253       263       273       283|  |   293    ||
                                                                                                                                             129-MSE                                          178-MSE                                                                                                   284-MSE       298|
                                                                                                                                                                                                                                                                                                           287-MSE     304

Legend:		→ Mismatch	(orange background)
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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( (-)

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Families(

)

Protein Domains( (-)

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Organisms( (-)

)

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

Fold: Chelatase-like (149)

Superfamily: Helical backbone metal receptor (102)

Family: automated matches (30)

Protein domain: automated matches (30)

Bacillus subtilis [TaxId: 224308] (2)

1a	d3gfva_	A:
1b	d3gfvb_	B:

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (YCLQ_BACSU | P94421)

biological process
	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:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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