3JT2 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CU(II) N47S/M121L VARIANT OF PSEUDOMONAS AERUGINOSA AZURIN

Authors :   Y. G. Gao, H. Robinson

Date :   11 Sep 09 (Deposition) - 17 Nov 09 (Release) - 17 Nov 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Cupredoxin, Azurin, Greek Key, Beta Barrel, Electron Transfer, Copper, Disulfide Bond, Electron Transport, Metal-Binding, Periplasm, Transport, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. M. Marshall, D. K. Garner, T. D. Wilson, Y. G. Gao, H. Robinson, M. J. Nilges, Y. Lu
Rationally Tuning The Reduction Potential Of A Single Cupredoxin Beyond The Natural Range.
Nature V. 462 113 2009
PubMed-ID: 19890331 | Reference-DOI: 10.1038/NATURE08551
(for further references see the PDB file header)

Molecule 1 - AZURIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-9A
	Expression System Strain	:	BL21 DE3*
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AZU, AZURIN, PA4922
	Mutation	:	YES
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287

		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 (1, 2)

No.	Name	Count	Type	Full Name
1	CU	2	Ligand/Ion	COPPER (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:45 , HIS A:46 , CYS A:112 , HIS A:117	BINDING SITE FOR RESIDUE CU A 129
2	AC2	SOFTWARE	GLY B:45 , HIS B:46 , CYS B:112 , HIS B:117	BINDING SITE FOR RESIDUE CU B 129

Asymmetric Unit

No.	Residues
1	A:3	-	A:26
2	B:3	-	B:26

(no "Cis Peptide Bond" information available for 3JT2)

(no "SAP(SNP)/Variant" information available for 3JT2)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AZUR_PSEAE	125-141	2	A:105-120 B:105-120

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AZUR_PSEAE	125-141	1	A:105-120 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AZUR_PSEAE	125-141	1	- B:105-120

(no "Exon" information available for 3JT2)

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:128
 aligned with AZUR_PSEAE | P00282 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:128
                                    30        40        50        60        70        80        90       100       110       120       130       140        
           AZUR_PSEAE    21 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTLK 148
               SCOP domains d3jt2a_ A: automated matches                                                                                                     SCOP domains
               CATH domains 3jt2A00 A:1-128 Cupredoxins -  blue copper proteins                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..........eeeee....eeeeeee.....hhhhhh...eeee..hhhhhhhhhhhhhhhhh........eeee........eeeeeee.hhh.....eeee..........eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------COPPER_BLUE      ------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jt2 A   1 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHSWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALLKGTLTLK 128
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:128
 aligned with AZUR_PSEAE | P00282 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:128
                                    30        40        50        60        70        80        90       100       110       120       130       140        
           AZUR_PSEAE    21 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTLK 148
               SCOP domains d3jt2b_ B: automated matches                                                                                                     SCOP domains
               CATH domains 3jt2B00 B:1-128 Cupredoxins -  blue copper proteins                                                                              CATH domains
           Pfam domains (1) Copper-bind-3jt2B01 B:1-128                                                                                                      Pfam domains (1)
           Pfam domains (2) Copper-bind-3jt2B02 B:1-128                                                                                                      Pfam domains (2)
         Sec.struct. author ...eeeee..........eeeee....eeeeeeee....hhhhhh...eeee..hhhhhhhhhhhhhhhhh........eeee.......eeeeeeee.hhh.....eeee..........eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------COPPER_BLUE      ------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jt2 B   1 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHSWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALLKGTLTLK 128
                                    10        20        30        40        50        60        70        80        90       100       110       120

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: All beta proteins (24004)

Fold: Cupredoxin-like (545)

Superfamily: Cupredoxins (543)

Family: Plastocyanin/azurin-like (241)

Protein domain: automated matches (22)

Pseudomonas aeruginosa [TaxId: 287] (5)

1a	d3jt2a_	A:
1b	d3jt2b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Cupredoxins - blue copper proteins (420)

Pseudomonas aeruginosa. Organism_taxid: 287. (36)

1a	3jt2A00	A:1-128
1b	3jt2B00	B:1-128

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CU_oxidase (192)

Family: Copper-bind (82)

Pseudomonas aeruginosa (25)

1a	Copper-bind-3jt2B01	B:1-128
1b	Copper-bind-3jt2B02	B:1-128

Asymmetric Unit(hide GO term definitions)

Chain A,B (AZUR_PSEAE | P00282)

molecular function
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0046914	transition metal ion binding	Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
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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Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

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