2FTA - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   STRUCTURE OF CU(II)AZURIN WITH THE METAL-BINDING LOOP SEQUENCE "CTFPGHSALM" REPLACED WITH "CTPHPFM"

Authors :   M. J. Banfield

Date :   24 Jan 06 (Deposition) - 11 Apr 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.61

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

Keywords :   Blue Copper-Binding Protein, Greek-Key Beta-Barrel, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Li, S. Yanagisawa, B. M. Martins, A. Messerschmidt, M. J. Banfield, C. Dennison
Basic Requirements For A Metal-Binding Site In A Protein: The Influence Of Loop Shortening On The Cupredoxin Azurin.
Proc. Natl. Acad. Sci. Usa V. 103 7258 2006
PubMed-ID: 16651527 | Reference-DOI: 10.1073/PNAS.0600774103
(for further references see the PDB file header)

Molecule 1 - AZURIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	TRK99A
	Expression System Strain	:	JM101
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AZU
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 10)

No.	Name	Count	Type	Full Name
1	2PE	2	Ligand/Ion	NONAETHYLENE GLYCOL
2	CU	4	Ligand/Ion	COPPER (II) ION
3	EOH	3	Ligand/Ion	ETHANOL
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	2PE	1	Ligand/Ion	NONAETHYLENE GLYCOL
2	CU	-1	Ligand/Ion	COPPER (II) ION
3	EOH	3	Ligand/Ion	ETHANOL
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	2PE	-1	Ligand/Ion	NONAETHYLENE GLYCOL
2	CU	-1	Ligand/Ion	COPPER (II) ION
3	EOH	-1	Ligand/Ion	ETHANOL
4	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	2PE	-1	Ligand/Ion	NONAETHYLENE GLYCOL
2	CU	-1	Ligand/Ion	COPPER (II) ION
3	EOH	-1	Ligand/Ion	ETHANOL
4	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	2PE	1	Ligand/Ion	NONAETHYLENE GLYCOL
2	CU	-1	Ligand/Ion	COPPER (II) ION
3	EOH	-1	Ligand/Ion	ETHANOL
4	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:45 , HIS A:46 , CYS A:112 , HIS A:115 , MET A:118	BINDING SITE FOR RESIDUE CU A 126
02	AC2	SOFTWARE	GLY B:45 , HIS B:46 , CYS B:112 , HIS B:115 , MET B:118	BINDING SITE FOR RESIDUE CU B 126
03	AC3	SOFTWARE	GLY C:45 , HIS C:46 , CYS C:112 , HIS C:115 , MET C:118	BINDING SITE FOR RESIDUE CU C 126
04	AC4	SOFTWARE	GLY D:45 , HIS D:46 , CYS D:112 , HIS D:115 , MET D:118	BINDING SITE FOR RESIDUE CU D 126
05	AC5	SOFTWARE	PRO A:116 , PHE A:117 , LYS A:119 , EOH A:502 , PEG A:504 , HOH A:562 , HOH A:612 , HOH A:614	BINDING SITE FOR RESIDUE 2PE A 501
06	AC6	SOFTWARE	GLN A:107 , MET D:109 , PHE D:117 , LYS D:119 , GLY D:120 , HOH D:578	BINDING SITE FOR RESIDUE 2PE D 505
07	AC7	SOFTWARE	GLN A:57 , 2PE A:501 , PEG A:504	BINDING SITE FOR RESIDUE EOH A 502
08	AC8	SOFTWARE	ASN A:18 , LYS A:119	BINDING SITE FOR RESIDUE EOH A 503
09	AC9	SOFTWARE	LYS A:74 , HOH A:605	BINDING SITE FOR RESIDUE EOH A 506
10	BC1	SOFTWARE	LYS A:119 , 2PE A:501 , EOH A:502 , HOH A:515	BINDING SITE FOR RESIDUE PEG A 504

Asymmetric Unit

No.	Residues
1	A:3	-	A:26
2	B:3	-	B:26
3	C:3	-	C:26
4	D:3	-	D:26

(no "Cis Peptide Bond" information available for 2FTA)

(no "SAP(SNP)/Variant" information available for 2FTA)

Asymmetric Unit (1, 4)

	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	4	A:105-118 B:105-118 C:105-118 D:105-118

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:105-118 - - -

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:105-118 - -

Biological Unit 3 (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	- - C:105-118 -

Biological Unit 4 (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	- - - D:105-118

(no "Exon" information available for 2FTA)

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:122
 aligned with AZUR_PSEAE | P00282 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:125
                                    32        42        52        62        72        82        92       102       112       122       132       142     
           AZUR_PSEAE    23 CSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTL 147
               SCOP domains d2ftaa_ A: Azurin                                                                                                             SCOP domains
               CATH domains 2ftaA00 A:3-124 Cupredoxins -  blue copper proteins                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..........eee......eeeeeee.....hhhhhh...eeee..hhhhhhhhhhhhhhhhh..........ee........eeeeeee.hhh.....eeeee.-.-e-eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------COPPER_BLUE      ------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fta A   3 CSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCT-P-H-PFMKGTLTL 124
                                    12        22        32        42        52        62        72        82        92       102       112| | | |119     
                                                                                                                                        113 | | |        
                                                                                                                                          114 | |        
                                                                                                                                            115 |        
                                                                                                                                              116

Chain B from PDB  Type:PROTEIN  Length:123
 aligned with AZUR_PSEAE | P00282 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:126
                                    31        41        51        61        71        81        91       101       111       121       131       141      
           AZUR_PSEAE    22 ECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTL 147
               SCOP domains d2ftab_ B: Azurin                                                                                                              SCOP domains
               CATH domains 2ftaB00 B:2-124 Cupredoxins -  blue copper proteins                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..........eee......eeeeeee.....hhhhhh...eeeehhhhhhhhhhhhhhhhhhh..........ee........eeeeeee.hhh.....eeee..-.-.-...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------COPPER_BLUE      ------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2fta B   2 ECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCT-P-H-PFMKGTLTL 124
                                    11        21        31        41        51        61        71        81        91       101       111 | | | 118      
                                                                                                                                         113 | | |        
                                                                                                                                           114 | |        
                                                                                                                                             115 |        
                                                                                                                                               116

Chain C from PDB  Type:PROTEIN  Length:124
 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 d2ftac_ C: Azurin                                                                                                               SCOP domains
               CATH domains 2ftaC00 C:2-125 Cupredoxins -  blue copper proteins                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..........eeeee....eeeeeee.....hhhhhh...eee...hhhhhhhhhhhhhhhhh..........ee........eeeeeee.hhh.....eeee..-.-.-...eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------COPPER_BLUE      ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fta C   2 ECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCT-P-H-PFMKGTLTLK 125
                                    11        21        31        41        51        61        71        81        91       101       111 | | | 118       
                                                                                                                                         113 | | |         
                                                                                                                                           114 | |         
                                                                                                                                             115 |         
                                                                                                                                               116

Chain D from PDB  Type:PROTEIN  Length:122
 aligned with AZUR_PSEAE | P00282 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:125
                                    32        42        52        62        72        82        92       102       112       122       132       142     
           AZUR_PSEAE    23 CSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTL 147
               SCOP domains d2ftad_ D: Azurin                                                                                                             SCOP domains
               CATH domains 2ftaD00 D:3-124 Cupredoxins -  blue copper proteins                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..........eee......eeeeeee.....hhhhhh...eeee..hhhhhhhhhhhhhhhhh..........ee........eeeeeee.hhh.....eeee..-.-.-...eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------COPPER_BLUE      ------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fta D   3 CSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCT-P-H-PFMKGTLTL 124
                                    12        22        32        42        52        62        72        82        92       102       112| | | |119     
                                                                                                                                        113 | | |        
                                                                                                                                          114 | |        
                                                                                                                                            115 |        
                                                                                                                                              116

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	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	d2ftaa_	A:
1b	d2ftab_	B:
1c	d2ftac_	C:
1d	d2ftad_	D:

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	2ftaC00	C:2-125
1b	2ftaB00	B:2-124
1c	2ftaA00	A:3-124
1d	2ftaD00	D:3-124

(no "Pfam Domain" information available for 2FTA)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (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).

Asymmetric Unit
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2ft6	STRUCTURE OF CU(II)AZURIN WITH THE METAL-BINDING LOOP SEQUENCE "CTFPGHSALM" REPLACED WITH "CTPHPM"
2ft7	CRYSTAL STRUCTURE OF CU(I)AZURIN AY PH6, WITH THE METAL- BINDING LOOP SEQUENCE "CTFPGHSALM" REPLACED WITH "CTPHPM
2ft8	CRYSTAL STRUCTURE OF CU(I)AZURIN, PH8, WITH THE METAL- BINDING LOOP SEQUENCE "CTFPGHSALM" REPLACED WITH "CTPHPM"

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