1XQ4 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE PUTATIVE APAA PROTEIN FROM BORDETELLA PERTUSSIS, NORTHEAST STRUCTURAL GENOMICS TARGET BER40

Authors :   F. Forouhar, W. Yong, S. M. Vorobiev, R. Xiao, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (Nesg)

Date :   11 Oct 04 (Deposition) - 09 Nov 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   All Beta Protein, Structural Genomics, Protein Structure Initiative, Psi, Northeast Structural Genomics Consortium, Nesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Forouhar, W. Yong, S. M. Vorobiev, R. Xiao, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong
Crystal Structure Of The Putative Apaa Protein From Bordetella Pertussis, Northeast Structural Genomics Target Ber40
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PROTEIN APAG
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21(BL21)
	Expression System Strain	:	BL21(DE3)+MAGIC
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	APAG
	Organism Scientific	:	BORDETELLA PERTUSSIS
	Organism Taxid	:	520

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 12)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
2	PO4	4	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:55 , ARG A:69 , THR A:104 , HIS A:106 , GLU A:116	BINDING SITE FOR RESIDUE PO4 A 401
2	AC2	SOFTWARE	HIS B:55 , ARG B:69 , THR B:104 , HIS B:106 , GLU B:116	BINDING SITE FOR RESIDUE PO4 B 402
3	AC3	SOFTWARE	HIS C:55 , ARG C:69 , THR C:104 , HIS C:106 , GLU C:116	BINDING SITE FOR RESIDUE PO4 C 403
4	AC4	SOFTWARE	HIS D:55 , ARG D:69 , THR D:104 , HIS D:106 , GLU D:116 , HOH D:425	BINDING SITE FOR RESIDUE PO4 D 404

(no "SS Bond" information available for 1XQ4)

(no "Cis Peptide Bond" information available for 1XQ4)

(no "SAP(SNP)/Variant" information available for 1XQ4)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	APAG	PS51087	ApaG domain profile.	APAG_BORPE	7-131	4	A:7-129 B:7-127 C:7-128 D:7-128

(no "Exon" information available for 1XQ4)

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
	(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:123
 aligned with APAG_BORPE | Q7VU61 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:123
                                    16        26        36        46        56        66        76        86        96       106       116       126   
           APAG_BORPE     7 PVKPYDLTVSVTPRYVPEQSDPSQQQYVFAYTVRITNTGSHPAQVISRHWIITDGEERVQEVRGLGVVGQQPLLAPGETFEYTSGCPLPTPIGTMRGTYHCVGENGIPFEVPIAEFLLAMPRT 129
               SCOP domains d1xq4a_ A: ApaG                                                                                                             SCOP domains
               CATH domains 1xq4A00 A:7-129 Protein apag                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee.hhhhhhhhh.eeeeeeeeeee.....eeeeeeeeeee.....eeeeeee.......ee....eeeeeeeeee...eeeeeeeeeeee....eeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE APAG  PDB: A:7-129 UniProt: 7-131                                                                                           PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xq4 A   7 PVKPYDLTVSVTPRYVPEQSDPSQQQYVFAYTVRITNTGSHPAQVISRHWIITDGEERVQEVRGLGVVGQQPLLAPGETFEYTSGCPLPTPIGTmRGTYHCVGENGIPFEVPIAEFLLAmPRT 129
                                    16        26        36        46        56        66        76        86        96    |  106       116       126   
                                                                                                                        101-MSE                  126-MSE

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with APAG_BORPE | Q7VU61 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:121
                                    16        26        36        46        56        66        76        86        96       106       116       126 
           APAG_BORPE     7 PVKPYDLTVSVTPRYVPEQSDPSQQQYVFAYTVRITNTGSHPAQVISRHWIITDGEERVQEVRGLGVVGQQPLLAPGETFEYTSGCPLPTPIGTMRGTYHCVGENGIPFEVPIAEFLLAMP 127
               SCOP domains d1xq4b_ B: ApaG                                                                                                           SCOP domains
               CATH domains 1xq4B00 B:7-127 Protein apag                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee...hhhhhhhhhh.eeeeeeeeeee.....eeeeeeeeeee.....eeeeeee.......ee....eeeeeeeeee...eeeeeeeeeeee....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE APAG  PDB: B:7-127 UniProt: 7-131                                                                                         PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xq4 B   7 PVKPYDLTVSVTPRYVPEQSDPSQQQYVFAYTVRITNTGSHPAQVISRHWIITDGEERVQEVRGLGVVGQQPLLAPGETFEYTSGCPLPTPIGTmRGTYHCVGENGIPFEVPIAEFLLAmP 127
                                    16        26        36        46        56        66        76        86        96    |  106       116       126 
                                                                                                                        101-MSE                  126-MSE

Chain C from PDB  Type:PROTEIN  Length:122
 aligned with APAG_BORPE | Q7VU61 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:122
                                    16        26        36        46        56        66        76        86        96       106       116       126  
           APAG_BORPE     7 PVKPYDLTVSVTPRYVPEQSDPSQQQYVFAYTVRITNTGSHPAQVISRHWIITDGEERVQEVRGLGVVGQQPLLAPGETFEYTSGCPLPTPIGTMRGTYHCVGENGIPFEVPIAEFLLAMPR 128
               SCOP domains d1xq4c_ C: ApaG                                                                                                            SCOP domains
               CATH domains 1xq4C00 C:7-128 Protein apag                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee.hhhh......eeeeeeeeeee.....eeeeeeeeeee.....eeeeeee.......ee....eeeeeeeeee...eeeeeeeeeeee....eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE APAG  PDB: C:7-128 UniProt: 7-131                                                                                          PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xq4 C   7 PVKPYDLTVSVTPRYVPEQSDPSQQQYVFAYTVRITNTGSHPAQVISRHWIITDGEERVQEVRGLGVVGQQPLLAPGETFEYTSGCPLPTPIGTmRGTYHCVGENGIPFEVPIAEFLLAmPR 128
                                    16        26        36        46        56        66        76        86        96    |  106       116       126  
                                                                                                                        101-MSE                  126-MSE

Chain D from PDB  Type:PROTEIN  Length:122
 aligned with APAG_BORPE | Q7VU61 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:122
                                    16        26        36        46        56        66        76        86        96       106       116       126  
           APAG_BORPE     7 PVKPYDLTVSVTPRYVPEQSDPSQQQYVFAYTVRITNTGSHPAQVISRHWIITDGEERVQEVRGLGVVGQQPLLAPGETFEYTSGCPLPTPIGTMRGTYHCVGENGIPFEVPIAEFLLAMPR 128
               SCOP domains d1xq4d_ D: ApaG                                                                                                            SCOP domains
               CATH domains 1xq4D00 D:7-128 Protein apag                                                                                               CATH domains
           Pfam domains (1) ---------------DUF525-1xq4D01 D:22-111                                                                   ----------------- Pfam domains (1)
           Pfam domains (2) ---------------DUF525-1xq4D02 D:22-111                                                                   ----------------- Pfam domains (2)
           Pfam domains (3) ---------------DUF525-1xq4D03 D:22-111                                                                   ----------------- Pfam domains (3)
           Pfam domains (4) ---------------DUF525-1xq4D04 D:22-111                                                                   ----------------- Pfam domains (4)
         Sec.struct. author ......eeeeeeeee.hhhhhhhhh.eeeeeeeeeee.....eeeeeeeeeee.....eeeeeee.......ee....eeeeeeeeee...eeeeeeeeeeee....eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE APAG  PDB: D:7-128 UniProt: 7-131                                                                                          PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xq4 D   7 PVKPYDLTVSVTPRYVPEQSDPSQQQYVFAYTVRITNTGSHPAQVISRHWIITDGEERVQEVRGLGVVGQQPLLAPGETFEYTSGCPLPTPIGTmRGTYHCVGENGIPFEVPIAEFLLAmPR 128
                                    16        26        36        46        56        66        76        86        96    |  106       116       126  
                                                                                                                        101-MSE                  126-MSE

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: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: ApaG-like (4)

Family: ApaG-like (4)

Protein domain: ApaG (4)

Bordetella pertussis [TaxId: 520] (1)

1a	d1xq4a_	A:
1b	d1xq4b_	B:
1c	d1xq4c_	C:
1d	d1xq4d_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Protein apag (4)

Bordetella pertussis. Organism_taxid: 520. (1)

1a	1xq4A00	A:7-129
1b	1xq4C00	C:7-128
1c	1xq4D00	D:7-128
1d	1xq4B00	B:7-127

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: DUF525] (3)

Family: DUF525 (3)

Bordetella pertussis (1)

1a	DUF525-1xq4D01	D:22-111
1b	DUF525-1xq4D02	D:22-111
1c	DUF525-1xq4D03	D:22-111
1d	DUF525-1xq4D04	D:22-111

Asymmetric/Biological Unit(hide GO term definitions)

(no "Gene Ontology" information available for 1XQ4)

Asymmetric/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 12)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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