1ID2 - JenaLib

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Title :   CRYSTAL STRUCTURE OF AMICYANIN FROM PARACOCCUS VERSUTUS (THIOBACILLUS VERSUTUS)

Authors :   A. Romero, H. Nar, A. Messerschmidt

Date :   03 Apr 01 (Deposition) - 11 Apr 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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

Keywords :   Beta Barrel, Type-1 Blue Copper Protein, Electron Transfer Protein, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Romero, H. Nar, R. Huber, A. Messerschmidt, A. P. Kalverda, G. W. Canters, R. Durley, F. S. Mathews
Crystal Structure Analysis And Refinement At 2. 15 A Resolution Of Amicyanin, A Type I Blue Copper Protein, From Thiobacillus Versutus.
J. Mol. Biol. V. 236 1196 1994
PubMed-ID: 8120896 | Reference-DOI: 10.1016/0022-2836(94)90021-3
(for further references see the PDB file header)

Molecule 1 - AMICYANIN
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PUC18
	Expression System Strain	:	JM105
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MAUC OR AMI
	Organism Scientific	:	PARACOCCUS VERSUTUS
	Organism Taxid	:	34007

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	CU	3	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

Biological Unit 3 (0, 0)

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

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:54 , CYS A:93 , HIS A:96 , MET A:99	BINDING SITE FOR RESIDUE CU A 107
2	AC2	SOFTWARE	HIS B:54 , CYS B:93 , HIS B:96 , MET B:99	BINDING SITE FOR RESIDUE CU B 107
3	AC3	SOFTWARE	HIS C:54 , CYS C:93 , HIS C:96 , MET C:99	BINDING SITE FOR RESIDUE CU C 107

(no "SS Bond" information available for 1ID2)

(no "Cis Peptide Bond" information available for 1ID2)

(no "SAP(SNP)/Variant" information available for 1ID2)

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.	AMCY_PARVE	112-125	3	A:86-99 B:86-99 C:86-99

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_PARVE	112-125	1	A:86-99 - -

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_PARVE	112-125	1	- B:86-99 -

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.	AMCY_PARVE	112-125	1	- - C:86-99

(no "Exon" information available for 1ID2)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:106
 aligned with AMCY_PARVE | P22365 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:106
                                    36        46        56        66        76        86        96       106       116       126      
           AMCY_PARVE    27 QDKITVTSEKPVAAADVPADAVVVGIEKMKYLTPEVTIKAGETVYWVNGEVMPHNVAFKKGIVGEDAFRGEMMTKDQAYAITFNEAGSYDYFCTPHPFMRGKVIVE 132
               SCOP domains d1id2a_ A: Amicyanin                                                                                       SCOP domains
               CATH domains 1id2A00 A:1-106 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
                 1id2 A   1 QDKITVTSEKPVAAADVPADAVVVGIEKMKYLTPEVTIKAGETVYWVNGEVMPHNVAFKKGIVGEDAFRGEMMTKDQAYAITFNEAGSYDYFCTPHPFMRGKVIVE 106
                                    10        20        30        40        50        60        70        80        90       100

Chain B from PDB  Type:PROTEIN  Length:106
 aligned with AMCY_PARVE | P22365 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:106
                                    36        46        56        66        76        86        96       106       116       126      
           AMCY_PARVE    27 QDKITVTSEKPVAAADVPADAVVVGIEKMKYLTPEVTIKAGETVYWVNGEVMPHNVAFKKGIVGEDAFRGEMMTKDQAYAITFNEAGSYDYFCTPHPFMRGKVIVE 132
               SCOP domains d1id2b_ B: Amicyanin                                                                                       SCOP domains
               CATH domains 1id2B00 B:1-106 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
                 1id2 B   1 QDKITVTSEKPVAAADVPADAVVVGIEKMKYLTPEVTIKAGETVYWVNGEVMPHNVAFKKGIVGEDAFRGEMMTKDQAYAITFNEAGSYDYFCTPHPFMRGKVIVE 106
                                    10        20        30        40        50        60        70        80        90       100

Chain C from PDB  Type:PROTEIN  Length:106
 aligned with AMCY_PARVE | P22365 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:106
                                    36        46        56        66        76        86        96       106       116       126      
           AMCY_PARVE    27 QDKITVTSEKPVAAADVPADAVVVGIEKMKYLTPEVTIKAGETVYWVNGEVMPHNVAFKKGIVGEDAFRGEMMTKDQAYAITFNEAGSYDYFCTPHPFMRGKVIVE 132
               SCOP domains d1id2c_ C: Amicyanin                                                                                       SCOP domains
               CATH domains 1id2C00 C:1-106 Cupredoxins -  blue copper proteins                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee......ee.hhh....eeeee........eeee...eeeeeee........ee.........ee.......eeeeeee...eeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------COPPER_BLUE   ------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1id2 C   1 QDKITVTSEKPVAAADVPADAVVVGIEKMKYLTPEVTIKAGETVYWVNGEVMPHNVAFKKGIVGEDAFRGEMMTKDQAYAITFNEAGSYDYFCTPHPFMRGKVIVE 106
                                    10        20        30        40        50        60        70        80        90       100

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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(

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Folds(

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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 versutus (Thiobacillus versutus) [TaxId: 34007] (1)

1a	d1id2a_	A:
1b	d1id2b_	B:
1c	d1id2c_	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)

Paracoccus versutus. Organism_taxid: 34007. (1)

1a	1id2A00	A:1-106
1b	1id2B00	B:1-106
1c	1id2C00	C:1-106

(no "Pfam Domain" information available for 1ID2)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (AMCY_PARVE | P22365)

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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