2W88 - JenaLib

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Title :   PLASTOCYANIN VARIANT WITH N-TERMINAL METHIONINE - OPEN STRUCTURE

Authors :   P. B. Crowley, P. M. Matias, A. R. Khan

Date :   14 Jan 09 (Deposition) - 27 Oct 09 (Release) - 26 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.89

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

Keywords :   Protein Interactions, Transport, Cupredoxin, Self-Assembly, Metal-Binding, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. B. Crowley, P. M. Matias, A. R. Khan, M. Roessle, D. I. Svergun
Metal-Mediated Self-Assembly Of A Beta-Sandwich Protein.
Chemistry V. 15 12672 2009
PubMed-ID: 19834935 | Reference-DOI: 10.1002/CHEM.200901410

Molecule 1 - PLASTOCYANIN
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Organism Scientific	:	PHORMIDIUM LAMINOSUM
	Organism Taxid	:	32059

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 10)

No.	Name	Count	Type	Full Name
1	CU	3	Ligand/Ion	COPPER (II) ION
2	ZN	7	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

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

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:39 , CYS A:89 , HIS A:92 , MET A:97	BINDING SITE FOR RESIDUE CU A 106
02	AC2	SOFTWARE	HIS A:61 , ASP B:44 , ASP B:45	BINDING SITE FOR RESIDUE ZN A 107
03	AC3	SOFTWARE	MET A:0 , GLU A:1 , HIS A:24 , ASP A:27	BINDING SITE FOR RESIDUE ZN A 108
04	AC4	SOFTWARE	HIS C:39 , CYS C:89 , HIS C:92 , MET C:97	BINDING SITE FOR RESIDUE CU B 106
05	AC5	SOFTWARE	ASP A:44 , ASP A:45 , HIS C:61	BINDING SITE FOR RESIDUE ZN B 107
06	AC6	SOFTWARE	MET C:0 , GLU C:1 , HIS C:24 , ASP C:27	BINDING SITE FOR RESIDUE ZN B 108
07	AC7	SOFTWARE	HIS B:39 , CYS B:89 , HIS B:92 , MET B:97	BINDING SITE FOR RESIDUE CU C 106
08	AC8	SOFTWARE	HIS B:61 , ASP C:44 , ASP C:45	BINDING SITE FOR RESIDUE ZN C 107
09	AC9	SOFTWARE	GLU B:1 , HIS B:24 , ASP B:27	BINDING SITE FOR RESIDUE ZN C 108
10	BC1	SOFTWARE	MET B:0	BINDING SITE FOR RESIDUE ZN C 109

(no "SS Bond" information available for 2W88)

Asymmetric Unit

No.	Residues
1	Glu A:17	-	Pro A:18
2	Pro A:37	-	Pro A:38
3	Glu B:17	-	Pro B:18
4	Pro B:37	-	Pro B:38
5	Glu C:17	-	Pro C:18
6	Pro C:37	-	Pro C:38

(no "SAP(SNP)/Variant" information available for 2W88)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	PLAS_PHOLA	116-131	3	A:82-97 B:82-97 C:82-97

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	PLAS_PHOLA	116-131	6	A:82-97 B:82-97 C:82-97

(no "Exon" information available for 2W88)

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:106
 aligned with PLAS_PHOLA | Q51883 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:106
                                    43        53        63        73        83        93       103       113       123       133      
           PLAS_PHOLA    34 AETFTVKMGADSGLLQFEPANVTVHPGDTVKWVNNKLPPHNILFDDKQVPGASKELADKLSHSQLMFSPGESYEITFSSDFPAGTYTYYCAPHRGAGMVGKITVEG 139
               SCOP domains d2w88a_ A: Plastocyanin                                                                                    SCOP domains
               CATH domains 2w88A00 A:0-105 Cupredoxins -  blue copper proteins                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee........ee..eeee....eeeeee.....eeeee.hhhhhhhhhhhhhhhheeeee.....eeeee.......eeeeee...hhhhh.eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------COPPER_BLUE     -------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2w88 A   0 METFTVKMGADSGLLQFEPANVTVHPGDTVKWVNNKLPPHNILFDDKQVPGASKELADKLSHSQLMFSPGESYEITFSSDFPAGTYTYYCAPHRGAGMVGKITVEG 105
                                     9        19        29        39        49        59        69        79        89        99

Chain B from PDB  Type:PROTEIN  Length:106
 aligned with PLAS_PHOLA | Q51883 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:106
                                    43        53        63        73        83        93       103       113       123       133      
           PLAS_PHOLA    34 AETFTVKMGADSGLLQFEPANVTVHPGDTVKWVNNKLPPHNILFDDKQVPGASKELADKLSHSQLMFSPGESYEITFSSDFPAGTYTYYCAPHRGAGMVGKITVEG 139
               SCOP domains d2w88b_ B: Plastocyanin                                                                                    SCOP domains
               CATH domains 2w88B00 B:0-105 Cupredoxins -  blue copper proteins                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee........ee..eeee....eeeeee.....eeeee.hhhhhhhhhhhhhhhheeeee.....eeeee.......eeeeee...hhhhh.eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------COPPER_BLUE     -------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2w88 B   0 METFTVKMGADSGLLQFEPANVTVHPGDTVKWVNNKLPPHNILFDDKQVPGASKELADKLSHSQLMFSPGESYEITFSSDFPAGTYTYYCAPHRGAGMVGKITVEG 105
                                     9        19        29        39        49        59        69        79        89        99

Chain C from PDB  Type:PROTEIN  Length:106
 aligned with PLAS_PHOLA | Q51883 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:106
                                    43        53        63        73        83        93       103       113       123       133      
           PLAS_PHOLA    34 AETFTVKMGADSGLLQFEPANVTVHPGDTVKWVNNKLPPHNILFDDKQVPGASKELADKLSHSQLMFSPGESYEITFSSDFPAGTYTYYCAPHRGAGMVGKITVEG 139
               SCOP domains d2w88c_ C: Plastocyanin                                                                                    SCOP domains
               CATH domains 2w88C00 C:0-105 Cupredoxins -  blue copper proteins                                                        CATH domains
           Pfam domains (1) ---Copper-bind-2w88C01 C:3-104                                                                           - Pfam domains (1)
           Pfam domains (2) ---Copper-bind-2w88C02 C:3-104                                                                           - Pfam domains (2)
           Pfam domains (3) ---Copper-bind-2w88C03 C:3-104                                                                           - Pfam domains (3)
         Sec.struct. author ..eeeeee........ee..eeee....eeeeee.....eee..hhhhhhhhhhhhhhhhheeeee.....eeeee.......eeeeee...hhhhh.eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------COPPER_BLUE     -------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2w88 C   0 METFTVKMGADSGLLQFEPANVTVHPGDTVKWVNNKLPPHNILFDDKQVPGASKELADKLSHSQLMFSPGESYEITFSSDFPAGTYTYYCAPHRGAGMVGKITVEG 105
                                     9        19        29        39        49        59        69        79        89        99

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: Plastocyanin (56)

Phormidium laminosum [TaxId: 32059] (8)

1a	d2w88a_	A:
1b	d2w88b_	B:
1c	d2w88c_	C:

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)

Phormidium laminosum. Organism_taxid: 32059. (3)

1a	2w88A00	A:0-105
1b	2w88B00	B:0-105
1c	2w88C00	C:0-105

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CU_oxidase (192)

Family: Copper-bind (82)

Phormidium laminosum (2)

1a	Copper-bind-2w88C01	C:3-104
1b	Copper-bind-2w88C02	C:3-104
1c	Copper-bind-2w88C03	C:3-104

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (PLAS_PHOLA | Q51883)

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.
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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0009579	thylakoid	A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.
	GO:0042651	thylakoid membrane	The pigmented membrane of any thylakoid.

Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:17 - Pro A:18	[ RasMol ]
		Glu B:17 - Pro B:18	[ RasMol ]
		Glu C:17 - Pro C:18	[ RasMol ]
		Pro A:37 - Pro A:38	[ RasMol ]
		Pro B:37 - Pro B:38	[ RasMol ]
		Pro C:37 - Pro C:38	[ RasMol ]

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	2w88
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	PLAS_PHOLA \| Q51883	:	1baw 2q5b 2w8c 3bqv 3cvb 3cvc 3cvd 4r0o

1baw	PLASTOCYANIN FROM PHORMIDIUM LAMINOSUM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 3)

Exons (0, 0)

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Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File