3U25 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF P. AERUGINOAS AZURIN CONTAINING A TYR-HIS HYDROGEN BONDED PAIR

Authors :   J. J. Warren, J. R. Winkler, H. B. Gray

Date :   30 Sep 11 (Deposition) - 28 Dec 11 (Release) - 13 Jun 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.18

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

Keywords :   Azurin, Cupredoxin, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. J. Warren, J. R. Winkler, H. B. Gray
Redox Properties Of Tyrosine And Related Molecules.
Febs Lett. V. 586 596 2012
PubMed-ID: 22210190 | Reference-DOI: 10.1016/J.FEBSLET.2011.12.014

Molecule 1 - AZURIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3A
	Expression System Strain	:	BL21DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 22-148
	Gene	:	AZU, 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 (2, 4)

No.	Name	Count	Type	Full Name
1	CU	2	Ligand/Ion	COPPER (II) ION
2	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:45 , HIS A:46 , CYS A:112 , HIS A:117 , MET A:121	BINDING SITE FOR RESIDUE CU A 1
2	AC2	SOFTWARE	GLU A:2 , CYS A:3 , LYS A:74 , ASP A:76 , VAL A:80 , HIS A:83 , HOH A:144 , HOH A:151 , HOH A:194	BINDING SITE FOR RESIDUE TRS A 129
3	AC3	SOFTWARE	GLY B:45 , HIS B:46 , CYS B:112 , HIS B:117 , MET B:121	BINDING SITE FOR RESIDUE CU B 129
4	AC4	SOFTWARE	GLU B:2 , CYS B:3 , LYS B:74 , ASP B:76 , ASP B:77 , HIS B:83 , HOH B:193 , HOH B:200 , HOH B:248	BINDING SITE FOR RESIDUE TRS B 1

Asymmetric Unit

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

(no "Cis Peptide Bond" information available for 3U25)

(no "SAP(SNP)/Variant" information available for 3U25)

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:105-121 B:105-121

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:105-121 -

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:105-121

(no "Exon" information available for 3U25)

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:127
 aligned with AZUR_PSEAE | P00282 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:127
                                    31        41        51        61        71        81        91       101       111       121       131       141       
           AZUR_PSEAE    22 ECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTLK 148
               SCOP domains d3u25a_ A: Azurin                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..........eeeee....eeeeeee.....hhhhhh...eeee..hhhhhhhhhhh.hhhhh..........ee........eeeeeee.hhh.....eeee..........eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------COPPER_BLUE      ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u25 A   2 ECSVDIQGNDQMQFNTNAHTVDKSCKQFTVNLSHPGNLPKNVMGHNYVLSTAADMQGVVTDGMASGLDKDFLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQFMFFCTFPGHSALMKGTLTLK 128
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain B from PDB  Type:PROTEIN  Length:127
 aligned with AZUR_PSEAE | P00282 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:127
                                    31        41        51        61        71        81        91       101       111       121       131       141       
           AZUR_PSEAE    22 ECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTLK 148
               SCOP domains d3u25b_ B: Azurin                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..........eeeee....eeeeeee.....hhhhhh...eeee..hhhhhhhhhhhhhhhhh..........ee........eeeeeee.hhh.....eeee..........eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------COPPER_BLUE      ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u25 B   2 ECSVDIQGNDQMQFNTNAHTVDKSCKQFTVNLSHPGNLPKNVMGHNYVLSTAADMQGVVTDGMASGLDKDFLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQFMFFCTFPGHSALMKGTLTLK 128
                                    11        21        31        41        51        61        71        81        91       101       111       121

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: Azurin (95)

Pseudomonas aeruginosa [TaxId: 287] (78)

1a	d3u25a_	A:
1b	d3u25b_	B:

(no "CATH Domain" information available for 3U25)

(no "Pfam Domain" information available for 3U25)

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 (2, 4)

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SS Bonds (2, 2)

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