1YK5 - JenaLib

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Title :   PYROCOCCUS ABYSSI RUBREDOXIN

Authors :   H. Bonisch, C. L. Schmidt, P. Bianco, R. Ladenstein

Date :   17 Jan 05 (Deposition) - 17 Jan 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.79

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

Reference :   H. Bonisch, C. L. Schmidt, P. Bianco, R. Ladenstein
Ultrahigh-Resolution Study On Pyrococcus Abyssi Rubredoxin. I. 0. 69 A X-Ray Structure Of Mutant W4L/R5S.
Acta Crystallogr. , Sect. D V. 61 990 2005
PubMed-ID: 15983423 | Reference-DOI: 10.1107/S090744490501293X
(for further references see the PDB file header)

Molecule 1 - RUBREDOXIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	RUB
	Organism Scientific	:	PYROCOCCUS ABYSSI
	Organism Taxid	:	29292
	Synonym	:	RD

		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 (1, 4)

No.	Name	Count	Type	Full Name
1	FE	4	Ligand/Ion	FE (III) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:6 , CYS A:9 , CYS A:39 , CYS A:42	BINDING SITE FOR RESIDUE FE A 54
2	AC2	SOFTWARE	CYS B:6 , CYS B:9 , CYS B:39 , CYS B:42	BINDING SITE FOR RESIDUE FE B 54
3	AC3	SOFTWARE	CYS C:6 , CYS C:9 , CYS C:39 , CYS C:42	BINDING SITE FOR RESIDUE FE C 54
4	AC4	SOFTWARE	CYS D:6 , CYS D:9 , CYS D:39 , CYS D:42	BINDING SITE FOR RESIDUE FE D 54

(no "SS Bond" information available for 1YK5)

(no "Cis Peptide Bond" information available for 1YK5)

(no "SAP(SNP)/Variant" information available for 1YK5)

Asymmetric Unit (2, 7)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RUBREDOXIN_LIKE	PS50903	Rubredoxin-like domain profile.	RUBR_PYRAB	1-52	3	A:1-52 B:1-52 D:1-52
2	RUBREDOXIN	PS00202	Rubredoxin signature.	RUBR_PYRAB	33-43	4	A:33-43 B:33-43 C:33-43 D:33-43

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RUBREDOXIN_LIKE	PS50903	Rubredoxin-like domain profile.	RUBR_PYRAB	1-52	1	A:1-52 - -
2	RUBREDOXIN	PS00202	Rubredoxin signature.	RUBR_PYRAB	33-43	1	A:33-43 - - -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RUBREDOXIN_LIKE	PS50903	Rubredoxin-like domain profile.	RUBR_PYRAB	1-52	1	- B:1-52 -
2	RUBREDOXIN	PS00202	Rubredoxin signature.	RUBR_PYRAB	33-43	1	- B:33-43 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RUBREDOXIN_LIKE	PS50903	Rubredoxin-like domain profile.	RUBR_PYRAB	1-52	0	- - -
2	RUBREDOXIN	PS00202	Rubredoxin signature.	RUBR_PYRAB	33-43	1	- - C:33-43 -

Biological Unit 4 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RUBREDOXIN_LIKE	PS50903	Rubredoxin-like domain profile.	RUBR_PYRAB	1-52	1	- - D:1-52
2	RUBREDOXIN	PS00202	Rubredoxin signature.	RUBR_PYRAB	33-43	1	- - - D:33-43

(no "Exon" information available for 1YK5)

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:53
 aligned with RUBR_PYRAB | Q9V099 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:53
                                    10        20        30        40        50   
            RUBR_PYRAB    1 MAKWRCKICGYIYDEDEGDPDNGISPGTKFEDLPDDWVCPLCGAPKSEFERIE 53
               SCOP domains d1yk5a_ A: Rubredoxin                                 SCOP domains
               CATH domains 1yk5A00 A:1-53  [code=2.20.28.10, no name defined]    CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....eee....hhhhh.....hhhhh...........hhh.eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                PROSITE (1) RUBREDOXIN_LIKE  PDB: A:1-52 UniProt: 1-52          - PROSITE (1)
                PROSITE (2) --------------------------------RUBREDOXIN ---------- PROSITE (2)
                 Transcript ----------------------------------------------------- Transcript
                  1yk5 A  1 MAKWRCKICGYIYDEDEGDPDNGISPGTKFEDLPDDWVCPLCGAPKSEFERIE 53
                                    10        20        30        40        50

Chain B from PDB  Type:PROTEIN  Length:53
 aligned with RUBR_PYRAB | Q9V099 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:53
                                    10        20        30        40        50   
            RUBR_PYRAB    1 MAKWRCKICGYIYDEDEGDPDNGISPGTKFEDLPDDWVCPLCGAPKSEFERIE 53
               SCOP domains d1yk5b_ B: Rubredoxin                                 SCOP domains
               CATH domains 1yk5B00 B:1-53  [code=2.20.28.10, no name defined]    CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....eee....hhhhh.....hhhhh...........hhh.eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                PROSITE (1) RUBREDOXIN_LIKE  PDB: B:1-52 UniProt: 1-52          - PROSITE (1)
                PROSITE (2) --------------------------------RUBREDOXIN ---------- PROSITE (2)
                 Transcript ----------------------------------------------------- Transcript
                  1yk5 B  1 MAKWRCKICGYIYDEDEGDPDNGISPGTKFEDLPDDWVCPLCGAPKSEFERIE 53
                                    10        20        30        40        50

Chain C from PDB  Type:PROTEIN  Length:52
 aligned with RUBR_PYRAB | Q9V099 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:52
                                    11        21        31        41        51  
            RUBR_PYRAB    2 AKWRCKICGYIYDEDEGDPDNGISPGTKFEDLPDDWVCPLCGAPKSEFERIE 53
               SCOP domains d1yk5c_ C: Rubredoxin                                SCOP domains
               CATH domains 1yk5C00 C:2-53  [code=2.20.28.10, no name defined]   CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eee....hhhhh.....hhhhh...........hhh.eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                PROSITE (1) RUBREDOXIN_LIKE  PDB: - UniProt: 1-52              - PROSITE (1)
                PROSITE (2) -------------------------------RUBREDOXIN ---------- PROSITE (2)
                 Transcript ---------------------------------------------------- Transcript
                  1yk5 C  2 AKWRCKICGYIYDEDEGDPDNGISPGTKFEDLPDDWVCPLCGAPKSEFERIE 53
                                    11        21        31        41        51

Chain D from PDB  Type:PROTEIN  Length:53
 aligned with RUBR_PYRAB | Q9V099 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:53
                                    10        20        30        40        50   
            RUBR_PYRAB    1 MAKWRCKICGYIYDEDEGDPDNGISPGTKFEDLPDDWVCPLCGAPKSEFERIE 53
               SCOP domains d1yk5d_ D: Rubredoxin                                 SCOP domains
               CATH domains 1yk5D00 D:1-53  [code=2.20.28.10, no name defined]    CATH domains
           Pfam domains (1) --Rubredoxin-1yk5D01 D:3-49                      ---- Pfam domains (1)
           Pfam domains (2) --Rubredoxin-1yk5D02 D:3-49                      ---- Pfam domains (2)
           Pfam domains (3) --Rubredoxin-1yk5D03 D:3-49                      ---- Pfam domains (3)
           Pfam domains (4) --Rubredoxin-1yk5D04 D:3-49                      ---- Pfam domains (4)
         Sec.struct. author ..eeee.....eee....hhhhh.....hhhhh...........hhh.eeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                PROSITE (1) RUBREDOXIN_LIKE  PDB: D:1-52 UniProt: 1-52          - PROSITE (1)
                PROSITE (2) --------------------------------RUBREDOXIN ---------- PROSITE (2)
                 Transcript ----------------------------------------------------- Transcript
                  1yk5 D  1 MAKWRCKICGYIYDEDEGDPDNGISPGTKFEDLPDDWVCPLCGAPKSEFERIE 53
                                    10        20        30        40        50

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: Small proteins (3458)

Fold: Rubredoxin-like (572)

Superfamily: Rubredoxin-like (127)

Family: Rubredoxin (85)

Protein domain: Rubredoxin (65)

Pyrococcus abyssi [TaxId: 29292] (3)

1a	d1yk5a_	A:
1b	d1yk5b_	B:
1c	d1yk5c_	C:
1d	d1yk5d_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Single Sheet (341)

Topology: Rubrerythrin, domain 2 (145)

Homologous Superfamily: [code=2.20.28.10, no name defined] (77)

Pyrococcus abyssi. Organism_taxid: 29292. (2)

1a	1yk5C00	C:2-53
1b	1yk5A00	A:1-53
1c	1yk5B00	B:1-53
1d	1yk5D00	D:1-53

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Rubredoxin (46)

Family: Rubredoxin (29)

Pyrococcus abyssi (strain GE5 / Orsay) (3)

1a	Rubredoxin-1yk5D01	D:3-49
1b	Rubredoxin-1yk5D02	D:3-49
1c	Rubredoxin-1yk5D03	D:3-49
1d	Rubredoxin-1yk5D04	D:3-49

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (RUBR_PYRAB | Q9V099)

molecular function
	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:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	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.

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	RUBR_PYRAB \| Q9V099	:	1yk4 2pya

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