3C7M - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF REDUCED DSBL

Authors :   C. U. Stirnimann, J. P. A. Grimshaw, R. Glockshuber, M. G. Grutter, G. Capitani

Date :   07 Feb 08 (Deposition) - 15 Jul 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

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

Keywords :   Redox Protein, Periplasm, Redox-Active Center, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. P. Grimshaw, C. U. Stirnimann, M. S. Brozzo, G. Malojcic, M. G. Grutter, G. Capitani, R. Glockshuber
Dsbl And Dsbi Form A Specific Dithiol Oxidase System For Periplasmic Arylsulfate Sulfotransferase In Uropathogenic Escherichia Coli.
J. Mol. Biol. V. 380 667 2008
PubMed-ID: 18565543 | Reference-DOI: 10.1016/J.JMB.2008.05.031
(for further references see the PDB file header)

Molecule 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDSBLCYT
	Expression System Strain	:	BL21(DE3)
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ESCHERICHIA COLI
	Strain	:	CFT073

		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 (4, 18)

No.	Name	Count	Type	Full Name
1	CD	6	Ligand/Ion	CADMIUM ION
2	CL	10	Ligand/Ion	CHLORIDE ION
3	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PGE	-1	Ligand/Ion	TRIETHYLENE GLYCOL

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:63 , ASP A:113 , ASP B:156	BINDING SITE FOR RESIDUE CD A 196
02	AC2	SOFTWARE	GLU A:109	BINDING SITE FOR RESIDUE CD A 197
03	AC3	SOFTWARE	ASP A:156 , GLU B:63 , ASP B:113	BINDING SITE FOR RESIDUE CD B 196
04	AC4	SOFTWARE	ASP A:183 , ASP A:187	BINDING SITE FOR RESIDUE CD A 198
05	AC5	SOFTWARE	HIS B:105	BINDING SITE FOR RESIDUE CD B 197
06	AC6	SOFTWARE	HIS A:105	BINDING SITE FOR RESIDUE CD A 199
07	AC7	SOFTWARE	GLU A:109	BINDING SITE FOR RESIDUE CL A 200
08	AC8	SOFTWARE	ASP A:183	BINDING SITE FOR RESIDUE CL A 201
09	AC9	SOFTWARE	GLU A:63 , ARG A:110 , ASP A:113 , ASP B:156 , LYS B:159	BINDING SITE FOR RESIDUE CL A 202
10	BC1	SOFTWARE	ASP A:156 , LYS A:159 , GLU B:63 , ARG B:110	BINDING SITE FOR RESIDUE CL A 203
11	BC2	SOFTWARE	TYR B:104 , LYS B:108 , ARG B:110	BINDING SITE FOR RESIDUE CL B 198
12	BC3	SOFTWARE	PRO B:30	BINDING SITE FOR RESIDUE CL B 199
13	BC4	SOFTWARE	TYR A:104 , LYS A:108 , ARG A:110	BINDING SITE FOR RESIDUE CL A 204
14	BC5	SOFTWARE	PRO A:30 , HIS A:105	BINDING SITE FOR RESIDUE CL A 205
15	BC6	SOFTWARE	LYS A:23 , PHE A:53 , PRO A:55 , PHE A:93 , LYS A:97	BINDING SITE FOR RESIDUE CL A 206
16	BC7	SOFTWARE	LYS B:23 , PHE B:53 , PRO B:55 , PHE B:93 , LYS B:97	BINDING SITE FOR RESIDUE CL B 200
17	BC8	SOFTWARE	ALA A:38	BINDING SITE FOR RESIDUE PGE A 207

(no "SS Bond" information available for 3C7M)

Asymmetric Unit

No.	Residues
1	Val A:163	-	Pro A:164
2	Val B:163	-	Pro B:164

(no "SAP(SNP)/Variant" information available for 3C7M)

(no "PROSITE Motif" information available for 3C7M)

(no "Exon" information available for 3C7M)

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:195
 aligned with DSBL_ECOL6 | P0A4L7 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:195
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217     
           DSBL_ECOL6    28 FTEGTDYMVLEKPIPNADKTLIKVFSYACPFCYKYDKAVTGPVSEKVKDIVAFTPFHLETKGEYGKQASEVFAVLINKDKAAGISLFDANSQFKKAKFAYYAAYHDKKERWSDGKDPAAFIKTGLDAAGMSQADFEAALKEPAVQETLEKWKASYDVAKIQGVPAYVVNGKYLIYTKSIKSIDAMADLIRELASK 222
               SCOP domains d3c7ma_ A: automated matches                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..........eeeeee...hhhhhhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhh.....eeee...eee.hhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c7m A   1 FTEGTDYMVLEKPIPNADKTLIKVFSYACPFCYKYDKAVTGPVSEKVKDIVAFTPFHLETKGEYGKQASEVFAVLINKDKAAGISLFDANSQFKKAKFAYYAAYHDKKERWSDGKDPAAFIKTGLDAAGMSQADFEAALKEPAVQETLEKWKASYDVAKIQGVPAYVVNGKYLIYTKSIKSIDAMADLIRELASK 195
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain B from PDB  Type:PROTEIN  Length:195
 aligned with DSBL_ECOL6 | P0A4L7 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:195
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217     
           DSBL_ECOL6    28 FTEGTDYMVLEKPIPNADKTLIKVFSYACPFCYKYDKAVTGPVSEKVKDIVAFTPFHLETKGEYGKQASEVFAVLINKDKAAGISLFDANSQFKKAKFAYYAAYHDKKERWSDGKDPAAFIKTGLDAAGMSQADFEAALKEPAVQETLEKWKASYDVAKIQGVPAYVVNGKYLIYTKSIKSIDAMADLIRELASK 222
               SCOP domains d3c7mb_ B: automated matches                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..........eeeeee...hhhhhhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhh.....eeee...eee.hhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c7m B   1 FTEGTDYMVLEKPIPNADKTLIKVFSYACPFCYKYDKAVTGPVSEKVKDIVAFTPFHLETKGEYGKQASEVFAVLINKDKAAGISLFDANSQFKKAKFAYYAAYHDKKERWSDGKDPAAFIKTGLDAAGMSQADFEAALKEPAVQETLEKWKASYDVAKIQGVPAYVVNGKYLIYTKSIKSIDAMADLIRELASK 195
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

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)

Escherichia coli [TaxId: 562] (3)

1a	d3c7ma_	A:
1b	d3c7mb_	B:

(no "CATH Domain" information available for 3C7M)

(no "Pfam Domain" information available for 3C7M)

Asymmetric Unit(hide GO term definitions)

Chain A,B (DSBL_ECOL6 | P0A4L7)

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: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).

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	Cis Peptide Bonds
		Val A:163 - Pro A:164	[ RasMol ]
		Val B:163 - Pro B:164	[ RasMol ]

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Description

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Chains, Units

Ligands, Modified Residues, Ions (4, 18)

Sites (17, 17)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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