1WTF - JenaLib

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Title :   CRYSTAL STRUCTURE OF BACILLUS THERMOPROTEOLYTICUS FERREDOXIN VARIANTS CONTAINING UNEXPECTED [3FE-4S] CLUSTER THAT IS LINKED TO COENZYME A AT 1.6 A RESOLUTION

Authors :   T. Shirakawa, Y. Takahashi, K. Wada, J. Hirota, T. Takao, D. Ohmori, K. Fukuyama

Date :   22 Nov 04 (Deposition) - 08 Nov 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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 :   3Fe-4S Cluster, Coenzyme A, Ferredoxin, Complex, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Shirakawa, Y. Takahashi, K. Wada, J. Hirota, T. Takao, D. Ohmori, K. Fukuyama
Identification Of Variant Molecules Of Bacillus Thermoproteolyticus Ferredoxin: Crystal Structure Reveals Bound Coenzyme A And An Unexpected [3Fe-4S] Cluster Associated With A Canonical [4Fe-4S] Ligand Motif
Biochemistry V. 44 12402 2005
PubMed-ID: 16156653 | Reference-DOI: 10.1021/BI0508441
(for further references see the PDB file header)

Molecule 1 - FERREDOXIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-21A(+)
	Expression System Strain	:	C41(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	BACILLUS THERMOPROTEOLYTICUS
	Organism Taxid	:	1427

		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 (3, 8)

No.	Name	Count	Type	Full Name
1	COA	1	Ligand/Ion	COENZYME A
2	F3S	4	Ligand/Ion	FE3-S4 CLUSTER
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	COA	1	Ligand/Ion	COENZYME A
2	F3S	1	Ligand/Ion	FE3-S4 CLUSTER
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	COA	-1	Ligand/Ion	COENZYME A
2	F3S	1	Ligand/Ion	FE3-S4 CLUSTER
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	COA	-1	Ligand/Ion	COENZYME A
2	F3S	1	Ligand/Ion	FE3-S4 CLUSTER
3	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	COA	-1	Ligand/Ion	COENZYME A
2	F3S	1	Ligand/Ion	FE3-S4 CLUSTER
3	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS B:8 , ASP B:39 , ASN B:40 , GLN B:41 , HOH B:1016 , HOH B:1025 , HOH B:1052 , HOH B:1098	BINDING SITE FOR RESIDUE SO4 B 82
2	AC2	SOFTWARE	HOH A:1101 , HOH A:1107 , HOH A:1122	BINDING SITE FOR RESIDUE SO4 A 82
3	AC3	SOFTWARE	ASP A:39 , ASN A:40 , GLN A:41 , HOH A:1011 , HOH A:1012 , HOH A:1063 , HOH A:1099 , HOH A:1197	BINDING SITE FOR RESIDUE SO4 A 83
4	AC4	SOFTWARE	ILE A:12 , CYS A:14 , GLY A:15 , ALA A:16 , HOH A:1061 , HOH A:1064 , HOH A:1077 , HOH A:1078 , HOH A:1087 , HOH A:1090 , HOH A:1113 , HOH A:1133 , HOH A:1145 , ILE B:12	BINDING SITE FOR RESIDUE COA A 105
5	AC5	SOFTWARE	CYS A:11 , ILE A:12 , ALA A:13 , CYS A:14 , GLY A:15 , ALA A:16 , CYS A:17 , CYS A:61 , THR A:63 , ILE A:66	BINDING SITE FOR RESIDUE F3S A 1001
6	AC6	SOFTWARE	CYS B:11 , ILE B:12 , CYS B:14 , GLY B:15 , ALA B:16 , CYS B:17 , TYR B:27 , CYS B:61 , THR B:63	BINDING SITE FOR RESIDUE F3S B 1002
7	AC7	SOFTWARE	CYS C:11 , ILE C:12 , CYS C:14 , GLY C:15 , ALA C:16 , CYS C:17 , TYR C:27 , CYS C:61 , THR C:63	BINDING SITE FOR RESIDUE F3S C 1003
8	AC8	SOFTWARE	CYS D:11 , ILE D:12 , ALA D:13 , CYS D:14 , GLY D:15 , ALA D:16 , CYS D:17 , TYR D:27 , CYS D:61 , THR D:63	BINDING SITE FOR RESIDUE F3S D 1004

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

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

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	4FE4S_FER_2	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.	FER_BACTH	2-30	4	A:2-30 B:2-30 C:2-30 D:2-30

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	4FE4S_FER_2	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.	FER_BACTH	2-30	1	A:2-30 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	4FE4S_FER_2	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.	FER_BACTH	2-30	1	- B:2-30 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	4FE4S_FER_2	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.	FER_BACTH	2-30	1	- - C:2-30 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	4FE4S_FER_2	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.	FER_BACTH	2-30	1	- - - D:2-30

(no "Exon" information available for 1WTF)

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:81
 aligned with FER_BACTH | P10245 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:81
                                    10        20        30        40        50        60        70        80 
             FER_BACTH    1 PKYTIVDKETCIACGACGAAAPDIYDYDEDGIAYVTLDDNQGIVEVPDILIDDMMDAFEGCPTDSIKVADEPFDGDPNKFE 81
               SCOP domains d1wtfa_ A: automated matches                                                      SCOP domains
               CATH domains 1wtfA00 A:1-81  [code=3.30.70.20, no name defined]                                CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee........hhhhhhh...eee.....eee...........hhhhhhhhhhhhhhh....eeee............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -4FE4S_FER_2  PDB: A:2-30     --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                  1wtf A  1 PKYTIVDKETCIACGACGAAAPDIYDYDEDGIAYVTLDDNQGIVEVPDILIDDMMDAFEGCPTDSIKVADEPFDGDPNKFE 81
                                    10        20        30        40        50        60        70        80

Chain B from PDB  Type:PROTEIN  Length:81
 aligned with FER_BACTH | P10245 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:81
                                    10        20        30        40        50        60        70        80 
             FER_BACTH    1 PKYTIVDKETCIACGACGAAAPDIYDYDEDGIAYVTLDDNQGIVEVPDILIDDMMDAFEGCPTDSIKVADEPFDGDPNKFE 81
               SCOP domains d1wtfb_ B: automated matches                                                      SCOP domains
               CATH domains 1wtfB00 B:1-81  [code=3.30.70.20, no name defined]                                CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee........hhhhhhh...eee.....eee...........hhhhhhhhhhhhhhh....eeee............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -4FE4S_FER_2  PDB: B:2-30     --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                  1wtf B  1 PKYTIVDKETCIACGACGAAAPDIYDYDEDGIAYVTLDDNQGIVEVPDILIDDMMDAFEGCPTDSIKVADEPFDGDPNKFE 81
                                    10        20        30        40        50        60        70        80

Chain C from PDB  Type:PROTEIN  Length:81
 aligned with FER_BACTH | P10245 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:81
                                    10        20        30        40        50        60        70        80 
             FER_BACTH    1 PKYTIVDKETCIACGACGAAAPDIYDYDEDGIAYVTLDDNQGIVEVPDILIDDMMDAFEGCPTDSIKVADEPFDGDPNKFE 81
               SCOP domains d1wtfc_ C: automated matches                                                      SCOP domains
               CATH domains 1wtfC00 C:1-81  [code=3.30.70.20, no name defined]                                CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee........hhhhhhh...eee.....eee...........hhhhhhhhhhhhhhh....eeee............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -4FE4S_FER_2  PDB: C:2-30     --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                  1wtf C  1 PKYTIVDKETCIACGACGAAAPDIYDYDEDGIAYVTLDDNQGIVEVPDILIDDMMDAFEGCPTDSIKVADEPFDGDPNKFE 81
                                    10        20        30        40        50        60        70        80

Chain D from PDB  Type:PROTEIN  Length:81
 aligned with FER_BACTH | P10245 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:81
                                    10        20        30        40        50        60        70        80 
             FER_BACTH    1 PKYTIVDKETCIACGACGAAAPDIYDYDEDGIAYVTLDDNQGIVEVPDILIDDMMDAFEGCPTDSIKVADEPFDGDPNKFE 81
               SCOP domains d1wtfd_ D: automated matches                                                      SCOP domains
               CATH domains 1wtfD00 D:1-81  [code=3.30.70.20, no name defined]                                CATH domains
           Pfam domains (1) -----Fer4_13-1wtfD01 D:6-68                                         ------------- Pfam domains (1)
           Pfam domains (2) -----Fer4_13-1wtfD02 D:6-68                                         ------------- Pfam domains (2)
           Pfam domains (3) -----Fer4_13-1wtfD03 D:6-68                                         ------------- Pfam domains (3)
           Pfam domains (4) -----Fer4_13-1wtfD04 D:6-68                                         ------------- Pfam domains (4)
         Sec.struct. author ..eeee........hhhhhhh...eee.....eee...........hhhhhhhhhhhhhhh....eeee............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -4FE4S_FER_2  PDB: D:2-30     --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                  1wtf D  1 PKYTIVDKETCIACGACGAAAPDIYDYDEDGIAYVTLDDNQGIVEVPDILIDDMMDAFEGCPTDSIKVADEPFDGDPNKFE 81
                                    10        20        30        40        50        60        70        80

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	-	→ 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: Alpha and beta proteins (a+b) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: 4Fe-4S ferredoxins (143)

Family: Single 4Fe-4S cluster ferredoxin (15)

Protein domain: automated matches (2)

Bacillus thermoproteolyticus [TaxId: 1427] (1)

1a	d1wtfa_	A:
1b	d1wtfb_	B:
1c	d1wtfc_	C:
1d	d1wtfd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.20, no name defined] (120)

Bacillus thermoproteolyticus. Organism_taxid: 1427. (3)

1a	1wtfA00	A:1-81
1b	1wtfB00	B:1-81
1c	1wtfC00	C:1-81
1d	1wtfD00	D:1-81

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: 4Fe-4S (51)

Family: Fer4_13 (5)

Bacillus thermoproteolyticus (1)

1a	Fer4_13-1wtfD01	D:6-68
1b	Fer4_13-1wtfD02	D:6-68
1c	Fer4_13-1wtfD03	D:6-68
1d	Fer4_13-1wtfD04	D:6-68

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (FER_BACTH | P10245)

molecular function
	GO:0051539	4 iron, 4 sulfur cluster binding	Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
	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:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	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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