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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE ANALYSIS OF FERREDOXIN FROM PLASMODIUM FALCIPARUM

Authors :   Y. Kimata-Ariga, G. Kurisu, T. Hase

Date :   04 Mar 02 (Deposition) - 30 Sep 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Electron Transport, Iron-Sulfur (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kimata-Ariga, G. Kurisu, T. Hase
Redox Power Generator Of A Nonphotosynthetic Plastid In Malaria Parasite
To Be Published
PubMed: search

Molecule 1 - FERREDOXIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTRC99A
	Expression System Strain	:	JM105
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-98
	Organism Scientific	:	PLASMODIUM FALCIPARUM
	Organism Taxid	:	36329
	Strain	:	3D7

		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, 4)

No.	Name	Count	Type	Full Name
1	FES	2	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
2	NA	2	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	FES	1	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
2	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	FES	1	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
2	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:96 , HOH B:1133	BINDING SITE FOR RESIDUE NA A 1501
2	AC2	SOFTWARE	HOH A:1521	BINDING SITE FOR RESIDUE NA A 1502
3	AC3	SOFTWARE	SER A:38 , CYS A:39 , ARG A:40 , GLY A:42 , SER A:43 , CYS A:44 , CYS A:47 , LEU A:75 , CYS A:77	BINDING SITE FOR RESIDUE FES A 1099
4	AC4	SOFTWARE	SER B:38 , CYS B:39 , ARG B:40 , GLY B:42 , SER B:43 , CYS B:44 , CYS B:47 , LEU B:75 , CYS B:77	BINDING SITE FOR RESIDUE FES B 1100

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

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

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	2FE2S_FER_2	PS51085	2Fe-2S ferredoxin-type iron-sulfur binding domain profile.	FER_PLAF7	99-189	2	A:3-93 B:3-93
2	2FE2S_FER_1	PS00197	2Fe-2S ferredoxin-type iron-sulfur binding region signature.	FER_PLAF7	135-143	2	A:39-47 B:39-47

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	2FE2S_FER_2	PS51085	2Fe-2S ferredoxin-type iron-sulfur binding domain profile.	FER_PLAF7	99-189	1	A:3-93 -
2	2FE2S_FER_1	PS00197	2Fe-2S ferredoxin-type iron-sulfur binding region signature.	FER_PLAF7	135-143	1	A:39-47 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	2FE2S_FER_2	PS51085	2Fe-2S ferredoxin-type iron-sulfur binding domain profile.	FER_PLAF7	99-189	1	- B:3-93
2	2FE2S_FER_1	PS00197	2Fe-2S ferredoxin-type iron-sulfur binding region signature.	FER_PLAF7	135-143	1	- B:39-47

(no "Exon" information available for 1IUE)

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:98
 aligned with FER_PLAF7 | Q8IED5 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:98
                                   106       116       126       136       146       156       166       176       186        
            FER_PLAF7    97 LFYNITLRTNDGEKKIECNEDEYILDASERQNVELPYSCRGGSCSTCAAKLVEGEVDNDDQSYLDEEQIKKKYILLCTCYPKSDCVIETHKEDELHDM 194
               SCOP domains d1iuea_ A: 2Fe-2S ferredoxin                                                                       SCOP domains
               CATH domains 1iueA00 A:1-98  [code=3.10.20.30, no name defined]                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..eeeeeeee...hhhhhhhhh................eeeeee..ee.......hhhhhhh.eee.hhhee...eeee..hhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --2FE2S_FER_2  PDB: A:3-93 UniProt: 99-189                                                   ----- PROSITE (1)
                PROSITE (2) --------------------------------------2FE2S_FER--------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 1iue A   1 AFYNITLRTNDGEKKIECNEDEYILDASERQNVELPYSCRGGSCSTCAAKLVEGEVDNDDQSYLDEEQIKKKYILLCTCYPKSDCVIETHKEDELHDM  98
                                    10        20        30        40        50        60        70        80        90

Chain B from PDB  Type:PROTEIN  Length:98
 aligned with FER_PLAF7 | Q8IED5 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:98
                                   106       116       126       136       146       156       166       176       186        
            FER_PLAF7    97 LFYNITLRTNDGEKKIECNEDEYILDASERQNVELPYSCRGGSCSTCAAKLVEGEVDNDDQSYLDEEQIKKKYILLCTCYPKSDCVIETHKEDELHDM 194
               SCOP domains d1iueb_ B: 2Fe-2S ferredoxin                                                                       SCOP domains
               CATH domains 1iueB00 B:1-98  [code=3.10.20.30, no name defined]                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..eeeeeeee...hhhhhhhhh................eeeeee..ee.......hhhhhhh.eee.hhhee...eeee..hhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --2FE2S_FER_2  PDB: B:3-93 UniProt: 99-189                                                   ----- PROSITE (1)
                PROSITE (2) --------------------------------------2FE2S_FER--------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 1iue B   1 AFYNITLRTNDGEKKIECNEDEYILDASERQNVELPYSCRGGSCSTCAAKLVEGEVDNDDQSYLDEEQIKKKYILLCTCYPKSDCVIETHKEDELHDM  98
                                    10        20        30        40        50        60        70        80        90

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(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: beta-Grasp (ubiquitin-like) (1032)

Superfamily: 2Fe-2S ferredoxin-like (174)

Family: 2Fe-2S ferredoxin-related (74)

Protein domain: 2Fe-2S ferredoxin (54)

Malaria parasite (Plasmodium falciparum) [TaxId: 5833] (1)

1a	d1iuea_	A:
1b	d1iueb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Ubiquitin-like (UB roll) (674)

Homologous Superfamily: [code=3.10.20.30, no name defined] (153)

Plasmodium falciparum 3d7. Organism_taxid: 36329. Strain: 3d7. (1)

1a	1iueA00	A:1-98
1b	1iueB00	B:1-98

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (FER_PLAF7 | Q8IED5)

molecular function
	GO:0051537	2 iron, 2 sulfur cluster binding	Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two 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: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.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0022900	electron transport chain	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: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:0020011	apicoplast	The plastid organelle found in apicomplexans.

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