1SFD - JenaLib

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Title :   OXIDIZED FORM OF AMICYANIN MUTANT P94F

Authors :   C. J. Carrell, D. Sun, S. Jiang, V. L. Davidson, F. S. Mathews

Date :   19 Feb 04 (Deposition) - 27 Jul 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   0.99

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

Keywords :   Blue Copper Protein, Beta Sandwich, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. J. Carrell, D. Sun, S. Jiang, V. L. Davidson, F. S. Mathews
Structural Studies Of Two Mutants Of Amicyanin From Paracoccus Denitrificans That Stabilize The Reduced State Of The Copper.
Biochemistry V. 43 9372 2004
PubMed-ID: 15260480 | Reference-DOI: 10.1021/BI049634Z
(for further references see the PDB file header)

Molecule 1 - AMICYANIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	MAUC, AMI
	Mutation	:	YES
	Organism Scientific	:	PARACOCCUS DENITRIFICANS
	Organism Taxid	:	266

		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, 7)

No.	Name	Count	Type	Full Name
1	CU	2	Ligand/Ion	COPPER (II) ION
2	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:53 , CYS A:92 , HIS A:95 , MET A:98	BINDING SITE FOR RESIDUE CU A 107
2	AC2	SOFTWARE	HIS B:53 , CYS B:92 , HIS B:95 , MET B:98	BINDING SITE FOR RESIDUE CU B 107
3	AC3	SOFTWARE	GLU A:49 , ALA A:50 , LYS A:74 , HOH A:536 , HOH A:568 , HOH A:591 , HOH A:712 , HOH A:713	BINDING SITE FOR RESIDUE SO4 A 501
4	AC4	SOFTWARE	GLU B:49 , ALA B:50 , LYS B:74 , HOH B:541 , HOH B:658 , HOH B:681	BINDING SITE FOR RESIDUE SO4 B 502
5	AC5	SOFTWARE	HOH A:573 , VAL B:58 , ALA B:59 , HOH B:514 , HOH B:544 , HOH B:614 , HOH B:627 , HOH B:682	BINDING SITE FOR RESIDUE SO4 B 503
6	AC6	SOFTWARE	HIS B:56 , LYS B:68 , HOH B:532 , HOH B:544 , HOH B:612 , HOH B:627 , HOH B:643 , HOH B:734	BINDING SITE FOR RESIDUE SO4 B 504
7	AC7	SOFTWARE	HIS A:56 , HOH A:534 , HOH A:567 , HOH A:596 , HOH A:615 , HOH A:695 , LYS B:38 , ALA B:50 , HOH B:576 , HOH B:674 , HOH B:706	BINDING SITE FOR RESIDUE SO4 A 505

(no "SS Bond" information available for 1SFD)

(no "Cis Peptide Bond" information available for 1SFD)

(no "SAP(SNP)/Variant" information available for 1SFD)

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.	AMCY_PARDE	111-124	2	A:85-98 B:85-98

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.	AMCY_PARDE	111-124	1	A:85-98 -

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.	AMCY_PARDE	111-124	1	- B:85-98

(no "Exon" information available for 1SFD)

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:105
 aligned with AMCY_PARDE | P22364 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:105
                                    36        46        56        66        76        86        96       106       116       126     
           AMCY_PARDE    27 DKATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHPFMRGKVVVE 131
               SCOP domains d1sfda_ A: Amicyanin                                                                                      SCOP domains
               CATH domains 1sfdA00 A:1-105 Cupredoxins -  blue copper proteins                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee......ee.hhh....eeeeee..ee...eeee....eeeeee........ee.........ee.......eeeeeee...eeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------COPPER_BLUE   ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1sfd A   1 DKATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTFHPFMRGKVVVE 105
                                    10        20        30        40        50        60        70        80        90       100

Chain B from PDB  Type:PROTEIN  Length:105
 aligned with AMCY_PARDE | P22364 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:105
                                    36        46        56        66        76        86        96       106       116       126     
           AMCY_PARDE    27 DKATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHPFMRGKVVVE 131
               SCOP domains d1sfdb_ B: Amicyanin                                                                                      SCOP domains
               CATH domains 1sfdB00 B:1-105 Cupredoxins -  blue copper proteins                                                       CATH domains
           Pfam domains (1) ----------------Copper-bind-1sfdB01 B:17-105                                                              Pfam domains (1)
           Pfam domains (2) ----------------Copper-bind-1sfdB02 B:17-105                                                              Pfam domains (2)
         Sec.struct. author ..ee......ee.hhh....eeeeee..ee...eeee....eeeeee........ee.........ee.......eeeeeee...eeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------COPPER_BLUE   ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1sfd B   1 DKATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTFHPFMRGKVVVE 105
                                    10        20        30        40        50        60        70        80        90       100

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: Amicyanin (34)

Paracoccus denitrificans [TaxId: 266] (33)

1a	d1sfda_	A:
1b	d1sfdb_	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)

Paracoccus denitrificans. Organism_taxid: 266. (20)

1a	1sfdA00	A:1-105
1b	1sfdB00	B:1-105

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CU_oxidase (192)

Family: Copper-bind (82)

Paracoccus denitrificans (11)

1a	Copper-bind-1sfdB01	B:17-105
1b	Copper-bind-1sfdB02	B:17-105

Asymmetric Unit(hide GO term definitions)

Chain A,B (AMCY_PARDE | P22364)

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: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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1sf3	STRUCTURE OF THE REDUCED FORM OF THE P94A MUTANT OF AMICYANIN
1sfd	OXIDIZED FORM OF AMICYANIN MUTANT P94F
1sfh	REDUCED STATE OF AMICYANIN MUTANT P94F

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Ligands, Modified Residues, Ions (2, 7)

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