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Title :   THE CRYSTAL STRUCTURE OF A THIOREDOXIN-RELATED PROTEIN FROM DESULFITOBACTERIUM HAFNIENSE DCB

Authors :   K. Tan, L. Volkart, M. Gu, J. N. Kinney, G. Babnigg, C. Kerfeld, A. Joachi Midwest Center For Structural Genomics (Mcsg)

Date :   17 Mar 09 (Deposition) - 12 May 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.99

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x),B (1x)
Biol. Unit 2: C (1x),D (1x)
Biol. Unit 3: A,B  (1x)
Biol. Unit 4: C,D  (1x)

Keywords :   Apc92103, Thioredoxin, Desulfitobacterium Hafniense Dcb, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Tan, L. Volkart, M. Gu, J. N. Kinney, G. Babnigg, C. Kerfeld, A. Joachimiak
The Crystal Structure Of A Thioredoxin-Related Protein From Desulfitobacterium Hafniense Dcb
To Be Published
PubMed: search

Molecule 1 - THIOREDOXIN DOMAIN PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG19
	Expression System Strain	:	PPK1037
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DESULFITOBACTERIUM HAFNIENSE, DHAF_4889
	Organism Scientific	:	DESULFITOBACTERIUM HAFNIENSE DCB-2
	Organism Taxid	:	272564
	Strain	:	DCB

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A (1x)	B (1x)
Biological Unit 2 (1x)	:			C (1x)	D (1x)
Biological Unit 3 (1x)	:	A	B
Biological Unit 4 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 16)

No.	Name	Count	Type	Full Name
1	MSE	16	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (1, 8)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 4 (1, 8)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 3GNJ)

Asymmetric Unit

No.	Residues
1	A:31	-	A:34
2	B:31	-	B:34
3	C:31	-	C:34
4	D:31	-	D:34

Asymmetric Unit

No.	Residues
1	Val A:74	-	Pro A:75
2	Val B:74	-	Pro B:75
3	Val C:74	-	Pro C:75
4	Val D:74	-	Pro D:75

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

(no "PROSITE Motif" information available for 3GNJ)

(no "Exon" information available for 3GNJ)

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:111
 aligned with B8G0E7_DESHD | B8G0E7 from UniProtKB/TrEMBL  Length:108

    Alignment length:111
                               1                                                                                                           
                               |     7        17        27        37        47        57        67        77        87        97       107 
         B8G0E7_DESHD     - ---MSLEKLDTNTFEQLIYDEGKACLVMFSRKNCHVCQKVTPVLEELRLNYEESFGFYYVDVEEEKTLFQRFSLKGVPQILYFKDGEYKGKMAGDVEDDEVEQMIADVLED 108
               SCOP domains d3gnja_ A: automated matches                                                                                    SCOP domains
               CATH domains 3gnjA00 A:-2-108 Glutaredoxin                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee.hhhhhhhhhh.....eeeeee...hhhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh......eeeeee..eeeeeee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 3gnj A  -2 SNAmSLEKLDTNTFEQLIYDEGKACLVmFSRKNCHVCQKVTPVLEELRLNYEESFGFYYVDVEEEKTLFQRFSLKGVPQILYFKDGEYKGKmAGDVEDDEVEQmIADVLED 108
                               |     7        17       |27        37        47        57        67        77        87 |      97   |   107 
                               |                      25-MSE                                                          89-MSE     101-MSE   
                               1-MSE

Chain B from PDB  Type:PROTEIN  Length:108
 aligned with B8G0E7_DESHD | B8G0E7 from UniProtKB/TrEMBL  Length:108

    Alignment length:108
                             1                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99        
         B8G0E7_DESHD     - -MSLEKLDTNTFEQLIYDEGKACLVMFSRKNCHVCQKVTPVLEELRLNYEESFGFYYVDVEEEKTLFQRFSLKGVPQILYFKDGEYKGKMAGDVEDDEVEQMIADVLE 107
               SCOP domains d3gnjb_ B: automated matches                                                                                 SCOP domains
               CATH domains 3gnjB00 B:0-107 Glutaredoxin                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee.hhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhhh.....eeeeeee...hhhhhhhh......eeeeee..eeeeeee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 3gnj B   0 AmSLEKLDTNTFEQLIYDEGKACLVmFSRKNCHVCQKVTPVLEELRLNYEESFGFYYVDVEEEKTLFQRFSLKGVPQILYFKDGEYKGKmAGDVEDDEVEQmIADVLE 107
                             |       9        19     |  29        39        49        59        69        79        89        99 |      
                             1-MSE                  25-MSE                                                          89-MSE     101-MSE

Chain C from PDB  Type:PROTEIN  Length:111
 aligned with B8G0E7_DESHD | B8G0E7 from UniProtKB/TrEMBL  Length:108

    Alignment length:111
                               1                                                                                                           
                               |     7        17        27        37        47        57        67        77        87        97       107 
         B8G0E7_DESHD     - ---MSLEKLDTNTFEQLIYDEGKACLVMFSRKNCHVCQKVTPVLEELRLNYEESFGFYYVDVEEEKTLFQRFSLKGVPQILYFKDGEYKGKMAGDVEDDEVEQMIADVLED 108
               SCOP domains d3gnjc_ C: automated matches                                                                                    SCOP domains
               CATH domains 3gnjC00 C:-2-108 Glutaredoxin                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee.hhhhhhhhhh.....eeeeee...hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh......eeeeee..eeeeeee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 3gnj C  -2 SNAmSLEKLDTNTFEQLIYDEGKACLVmFSRKNCHVCQKVTPVLEELRLNYEESFGFYYVDVEEEKTLFQRFSLKGVPQILYFKDGEYKGKmAGDVEDDEVEQmIADVLED 108
                               |     7        17       |27        37        47        57        67        77        87 |      97   |   107 
                               1-MSE                  25-MSE                                                          89-MSE     101-MSE

Chain D from PDB  Type:PROTEIN  Length:110
 aligned with B8G0E7_DESHD | B8G0E7 from UniProtKB/TrEMBL  Length:108

    Alignment length:110
                              1                                                                                                           
                              |      8        18        28        38        48        58        68        78        88        98       108
         B8G0E7_DESHD     - --MSLEKLDTNTFEQLIYDEGKACLVMFSRKNCHVCQKVTPVLEELRLNYEESFGFYYVDVEEEKTLFQRFSLKGVPQILYFKDGEYKGKMAGDVEDDEVEQMIADVLED 108
               SCOP domains d3gnjd_ D: automated matches                                                                                   SCOP domains
               CATH domains 3gnjD00 D:-1-108 Glutaredoxin                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.hhhhhhhhhhh....eeeeee...hhhhhhhhhhhhhhhh......eeeeee...hhhhhhhh......eeeeee..eeeeeee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 3gnj D  -1 NAmSLEKLDTNTFEQLIYDEGKACLVmFSRKNCHVCQKVTPVLEELRLNYEESFGFYYVDVEEEKTLFQRFSLKGVPQILYFKDGEYKGKmAGDVEDDEVEQmIADVLED 108
                              |      8        18      | 28        38        48        58        68        78        88|       98  |    108
                              1-MSE                  25-MSE                                                          89-MSE     101-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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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)

Desulfitobacterium hafniense [TaxId: 272564] (1)

1a	d3gnja_	A:
1b	d3gnjb_	B:
1c	d3gnjc_	C:
1d	d3gnjd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Glutaredoxin (620)

Homologous Superfamily: Glutaredoxin (617)

Desulfitobacterium hafniense dcb-2. Organism_taxid: 272564. Strain: dcb. (1)

1a	3gnjA00	A:-2-108
1b	3gnjC00	C:-2-108
1c	3gnjD00	D:-1-108
1d	3gnjB00	B:0-107

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (B8G0E7_DESHD | B8G0E7)

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:0006662	glycerol ether metabolic process	The chemical reactions and pathways involving glycerol ethers, any anhydride formed between two organic hydroxy compounds, one of which is glycerol.
	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:0005623	cell	The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

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	Sites
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	Cis Peptide Bonds
		Val A:74 - Pro A:75	[ RasMol ]
		Val B:74 - Pro B:75	[ RasMol ]
		Val C:74 - Pro C:75	[ RasMol ]
		Val D:74 - Pro D:75	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (1, 16)

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SS Bonds (4, 4)

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