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Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A THIOL:DISULFIDE INTERCHANGE PROTEIN DSBA FROM BORDETELLA PARAPERTUSSIS

Authors :   K. Palani, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   06 May 09 (Deposition) - 19 May 09 (Release) - 19 May 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

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

Keywords :   Crystal Structure, Dsba, Protein Structure Initiative Ii(Psi Ii), Nysgxrc, 11213N, Structural Genomics, New York Sgx Research Center For Structural Genomics, Disulfide Bond, Periplasm, Redox-Active Center, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Palani, S. K. Burley, S. Swaminathan
Crystal Structure Of A Thiol:Disulfide Interchange Protein Dsba From Bordetella Parapertussis
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	BC-PSGX3 (BC)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	BPP4354, DSBA
	Organism Scientific	:	BORDETELLA PARAPERTUSSIS
	Organism Taxid	:	519
	Synonym	:	DISULFIDE-BOND FORMATION, THIOREDOXIN FAMILY

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 15)

No.	Name	Count	Type	Full Name
1	MSE	15	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 3HD5)

(no "SS Bond" information available for 3HD5)

Asymmetric/Biological Unit

No.	Residues
1	Asn A:37	-	Pro A:38
2	Thr A:173	-	Pro A:174
3	Asn B:37	-	Pro B:38
4	Thr B:173	-	Pro B:174
5	Asn C:37	-	Pro C:38
6	Thr C:173	-	Pro C:174

(no "SAP(SNP)/Variant" information available for 3HD5)

Asymmetric/Biological Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	DSBA_BORPA	50-68	3	A:50-68 B:50-68 C:50-68

(no "Exon" information available for 3HD5)

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:182
 aligned with DSBA_BORPA | Q7W2Q0 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:182
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207  
           DSBA_BORPA    28 QGAQQYVNINPPMPSDTPGKIEVLEFFAYTCPHCAAIEPMVEDWAKTAPQDVVLKQVPIAFNAGMKPLQQLYYTLQALERPDLHPKVFTAIHTERKRLFDKKAMGEWAASQGVDRAKFDSVFDSFSVQTQVQRASQLAEAAHIDGTPAFAVGGRYMTSPVLAGNDYAGALKVVDQLIVQSRK 209
               SCOP domains d3hd5a_ A: automated matches                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee............eeeeeee...hhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhh......hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee...eee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------THIOREDOXIN_1      --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hd5 A  28 QGAQQYVNINPPmPSDTPGKIEVLEFFAYTCPHCAAIEPmVEDWAKTAPQDVVLKQVPIAFNAGmKPLQQLYYTLQALERPDLHPKVFTAIHTERKRLFDKKAmGEWAASQGVDRAKFDSVFDSFSVQTQVQRASQLAEAAHIDGTPAFAVGGRYmTSPVLAGNDYAGALKVVDQLIVQSRE 209
                                    37  |     47        57        67        77        87    |   97       107       117       127   |   137       147       157       167       177     | 187       197       207  
                                       40-MSE                     67-MSE                   92-MSE                                131-MSE                                             183-MSE

Chain B from PDB  Type:PROTEIN  Length:179
 aligned with DSBA_BORPA | Q7W2Q0 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:179
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         
           DSBA_BORPA    31 QQYVNINPPMPSDTPGKIEVLEFFAYTCPHCAAIEPMVEDWAKTAPQDVVLKQVPIAFNAGMKPLQQLYYTLQALERPDLHPKVFTAIHTERKRLFDKKAMGEWAASQGVDRAKFDSVFDSFSVQTQVQRASQLAEAAHIDGTPAFAVGGRYMTSPVLAGNDYAGALKVVDQLIVQSRK 209
               SCOP domains d3hd5b_ B: automated matches                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee............eeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhh......hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee...eeehhhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------THIOREDOXIN_1      --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hd5 B  31 QQYVNINPPmPSDTPGKIEVLEFFAYTCPHCAAIEPmVEDWAKTAPQDVVLKQVPIAFNAGmKPLQQLYYTLQALERPDLHPKVFTAIHTERKRLFDKKAmGEWAASQGVDRAKFDSVFDSFSVQTQVQRASQLAEAAHIDGTPAFAVGGRYmTSPVLAGNDYAGALKVVDQLIVQSRE 209
                                    40        50        60      | 70        80        90 |     100       110       120       130|      140       150       160       170       180  |    190       200         
                                    40-MSE                     67-MSE                   92-MSE                                131-MSE                                             183-MSE

Chain C from PDB  Type:PROTEIN  Length:181
 aligned with DSBA_BORPA | Q7W2Q0 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:181
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208 
           DSBA_BORPA    29 GAQQYVNINPPMPSDTPGKIEVLEFFAYTCPHCAAIEPMVEDWAKTAPQDVVLKQVPIAFNAGMKPLQQLYYTLQALERPDLHPKVFTAIHTERKRLFDKKAMGEWAASQGVDRAKFDSVFDSFSVQTQVQRASQLAEAAHIDGTPAFAVGGRYMTSPVLAGNDYAGALKVVDQLIVQSRK 209
               SCOP domains d3hd5c_ C: automated matches                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee............eeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhhh....hhhhhhhhhhh......hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee...eee.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------THIOREDOXIN_1      --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hd5 C  29 GAQQYVNINPPmPSDTPGKIEVLEFFAYTCPHCAAIEPmVEDWAKTAPQDVVLKQVPIAFNAGmKPLQQLYYTLQALERPDLHPKVFTAIHTERKRLFDKKAmGEWAASQGVDRAKFDSVFDSFSVQTQVQRASQLAEAAHIDGTPAFAVGGRYmTSPVLAGNDYAGALKVVDQLIVQSRE 209
                                    38 |      48        58        68        78        88   |    98       108       118       128  |    138       148       158       168       178    |  188       198       208 
                                      40-MSE                     67-MSE                   92-MSE                                131-MSE                                             183-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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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

Fold: Thioredoxin fold (994)

Superfamily: Thioredoxin-like (992)

Family: automated matches (347)

Protein domain: automated matches (347)

Bordetella parapertussis [TaxId: 519] (1)

1a	d3hd5a_	A:
1b	d3hd5b_	B:
1c	d3hd5c_	C:

(no "CATH Domain" information available for 3HD5)

(no "Pfam Domain" information available for 3HD5)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (DSBA_BORPA | Q7W2Q0)

molecular function
	GO:0015035	protein disulfide oxidoreductase activity	Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	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:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric/Biological Unit
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	Sites
(no "Sites" information available for 3hd5)

	Cis Peptide Bonds
		Asn A:37 - Pro A:38	[ RasMol ]
		Asn B:37 - Pro B:38	[ RasMol ]
		Asn C:37 - Pro C:38	[ RasMol ]
		Thr A:173 - Pro A:174	[ RasMol ]
		Thr B:173 - Pro B:174	[ RasMol ]
		Thr C:173 - Pro C:174	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (1, 15)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

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