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Biological Unit 3 (Jmol Viewer)

Title :   RUBREDOXIN FROM DESULFOVIBRIO VULGARIS MIYAZAKI F, MONOCLINIC CRYSTAL FORM

Authors :   Y. Higuchi, N. Yasuoka

Date :   07 Oct 98 (Deposition) - 18 May 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Rubredoxin, Compnd, Electron Transfer Protein, Metalloprotein, Sulfate-Reducing Bacterium (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Misaki, Y. Morimoto, M. Ogata, T. Yagi, Y. Higuchi, N. Yasuoka
Structure Determination Of Rubredoxin From Desulfovibrio Vulgaris Miyazaki F In Two Crystal Forms.
Acta Crystallogr. , Sect. D V. 55 408 1999
PubMed-ID: 10089348 | Reference-DOI: 10.1107/S0907444998011810
(for further references see the PDB file header)

Molecule 1 - RUBREDOXIN
	Chains	:	A, B, C
	Organism Scientific	:	DESULFOVIBRIO VULGARIS STR. 'MIYAZAKI F'
	Organism Taxid	:	883
	Other Details	:	IAM 12604
	Strain	:	MIYAZAKI F

		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	FE	3	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

Asymmetric Unit (6, 6)

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 53
2	AC2	SOFTWARE	CYS B:6 , CYS B:9 , CYS B:39 , CYS B:42	BINDING SITE FOR RESIDUE FE B 53
3	AC3	SOFTWARE	CYS C:6 , CYS C:9 , CYS C:39 , CYS C:42	BINDING SITE FOR RESIDUE FE C 53
4	FEA	UNKNOWN	CYS A:6 , CYS A:9 , CYS A:39 , CYS A:42	FE COORDINATION SITE, CHAIN A.
5	FEB	UNKNOWN	CYS B:6 , CYS B:9 , CYS B:39 , CYS B:42	FE COORDINATION SITE, CHAIN B.
6	FEC	UNKNOWN	CYS C:6 , CYS C:9 , CYS C:39 , CYS C:42	FE COORDINATION SITE, CHAIN C.

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

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

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

Asymmetric Unit (2, 6)

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

Biological Unit 3 (2, 2)

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

(no "Exon" information available for 2RDV)

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
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Chain A from PDB  Type:PROTEIN  Length:52
 aligned with RUBR_DESVM | P15412 from UniProtKB/Swiss-Prot  Length:52

    Alignment length:52
                                    10        20        30        40        50  
            RUBR_DESVM    1 MKKYVCTVCGYEYDPAEGDPDNGVKPGTAFEDVPADWVCPICGAPKSEFEPA 52
               SCOP domains d2rdva_ A: Rubredoxin                                SCOP domains
               CATH domains 2rdvA00 A:1-52  [code=2.20.28.10, no name defined]   CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.............hhh.......hhh.............hhheee. 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
                  2rdv A  1 MKKYVCTVCGYEYDPAEGDPDNGVKPGTAFEDVPADWVCPICGAPKSEFEPA 52
                                    10        20        30        40        50

Chain B from PDB  Type:PROTEIN  Length:52
 aligned with RUBR_DESVM | P15412 from UniProtKB/Swiss-Prot  Length:52

    Alignment length:52
                                    10        20        30        40        50  
            RUBR_DESVM    1 MKKYVCTVCGYEYDPAEGDPDNGVKPGTAFEDVPADWVCPICGAPKSEFEPA 52
               SCOP domains d2rdvb_ B: Rubredoxin                                SCOP domains
               CATH domains 2rdvB00 B:1-52  [code=2.20.28.10, no name defined]   CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.............hhh.......hhh.............hhheee. 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
                  2rdv B  1 MKKYVCTVCGYEYDPAEGDPDNGVKPGTAFEDVPADWVCPICGAPKSEFEPA 52
                                    10        20        30        40        50

Chain C from PDB  Type:PROTEIN  Length:52
 aligned with RUBR_DESVM | P15412 from UniProtKB/Swiss-Prot  Length:52

    Alignment length:52
                                    10        20        30        40        50  
            RUBR_DESVM    1 MKKYVCTVCGYEYDPAEGDPDNGVKPGTAFEDVPADWVCPICGAPKSEFEPA 52
               SCOP domains d2rdvc_ C: Rubredoxin                                SCOP domains
               CATH domains 2rdvC00 C:1-52  [code=2.20.28.10, no name defined]   CATH domains
           Pfam domains (1) --Rubredoxin-2rdvC01 C:3-49                      --- Pfam domains (1)
           Pfam domains (2) --Rubredoxin-2rdvC02 C:3-49                      --- Pfam domains (2)
           Pfam domains (3) --Rubredoxin-2rdvC03 C:3-49                      --- Pfam domains (3)
         Sec.struct. author ..eeee.............hhh.......hhh.............hhheeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                PROSITE (1) RUBREDOXIN_LIKE  PDB: C:1-52 UniProt: 1-52           PROSITE (1)
                PROSITE (2) --------------------------------RUBREDOXIN --------- PROSITE (2)
                 Transcript ---------------------------------------------------- Transcript
                  2rdv C  1 MKKYVCTVCGYEYDPAEGDPDNGVKPGTAFEDVPADWVCPICGAPKSEFEPA 52
                                    10        20        30        40        50

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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: Small proteins (3458)

Fold: Rubredoxin-like (572)

Superfamily: Rubredoxin-like (127)

Family: Rubredoxin (85)

Protein domain: Rubredoxin (65)

Desulfovibrio vulgaris [TaxId: 881] (7)

1a	d2rdva_	A:
1b	d2rdvb_	B:
1c	d2rdvc_	C:

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)

'miyazaki f' (Desulfovibrio vulgaris str) (2)

1a	2rdvA00	A:1-52
1b	2rdvB00	B:1-52
1c	2rdvC00	C:1-52

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Rubredoxin (46)

Family: Rubredoxin (29)

Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637) (2)

1a	Rubredoxin-2rdvC01	C:3-49
1b	Rubredoxin-2rdvC02	C:3-49
1c	Rubredoxin-2rdvC03	C:3-49

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (RUBR_DESVM | P15412)

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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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