1GAO - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE L44S MUTANT OF FERREDOXIN I

Authors :   C. D. Stout, B. K. Burgess, G. S. Prasad, V. Sridhar, Y. S. Jung

Date :   30 Nov 00 (Deposition) - 13 Dec 00 (Release) - 31 Mar 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Reference :   K. Chen, Y. S. Jung, C. A. Bonagura, G. J. Tilley, G. S. Prasad, V. Sridhar, F. A. Armstrong, C. D. Stout, B. K. Burgess
Azotobacter Vinelandii Ferredoxin I: A Sequence And Structure Comparison Approach To Alteration Of [4Fe-4S]2+/+ Reduction Potential.
J. Biol. Chem. V. 277 5603 2002
PubMed-ID: 11704670 | Reference-DOI: 10.1074/JBC.M108916200
(for further references see the PDB file header)

Molecule 1 - FERREDOXIN I
	Chains	:	A, B, C, D
	Organism Scientific	:	AZOTOBACTER VINELANDII
	Organism Taxid	:	354

		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 (2, 8)

No.	Name	Count	Type	Full Name
1	F3S	4	Ligand/Ion	FE3-S4 CLUSTER
2	SF4	4	Ligand/Ion	IRON/SULFUR CLUSTER

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	F3S	1	Ligand/Ion	FE3-S4 CLUSTER
2	SF4	1	Ligand/Ion	IRON/SULFUR CLUSTER

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	F3S	1	Ligand/Ion	FE3-S4 CLUSTER
2	SF4	1	Ligand/Ion	IRON/SULFUR CLUSTER

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	F3S	1	Ligand/Ion	FE3-S4 CLUSTER
2	SF4	1	Ligand/Ion	IRON/SULFUR CLUSTER

Biological Unit 4 (2, 2)

No.	Name	Count	Type	Full Name
1	F3S	1	Ligand/Ion	FE3-S4 CLUSTER
2	SF4	1	Ligand/Ion	IRON/SULFUR CLUSTER

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:2 , CYS A:20 , PRO A:21 , VAL A:22 , CYS A:24 , ILE A:34 , CYS A:39 , ILE A:40 , CYS A:42 , ALA A:43 , CYS A:45	BINDING SITE FOR RESIDUE SF4 A 107
2	AC2	SOFTWARE	VAL A:4 , CYS A:8 , LYS A:12 , TYR A:13 , THR A:14 , ASP A:15 , CYS A:16 , LEU A:32 , CYS A:49 , ALA A:51 , ILE A:54	BINDING SITE FOR RESIDUE F3S A 108
3	AC3	SOFTWARE	CYS B:220 , CYS B:224 , PHE B:225 , ILE B:234 , CYS B:239 , ILE B:240 , CYS B:242 , ALA B:243 , CYS B:245	BINDING SITE FOR RESIDUE SF4 B 307
4	AC4	SOFTWARE	CYS B:208 , LYS B:212 , TYR B:213 , THR B:214 , ASP B:215 , CYS B:216 , CYS B:249	BINDING SITE FOR RESIDUE F3S B 308
5	AC5	SOFTWARE	PHE C:402 , CYS C:420 , CYS C:424 , ILE C:434 , CYS C:439 , ILE C:440 , CYS C:442 , ALA C:443 , CYS C:445	BINDING SITE FOR RESIDUE SF4 C 507
6	AC6	SOFTWARE	CYS C:408 , LYS C:412 , TYR C:413 , THR C:414 , ASP C:415 , CYS C:416 , CYS C:449 , PRO C:450 , ALA C:451 , ILE C:454	BINDING SITE FOR RESIDUE F3S C 508
7	AC7	SOFTWARE	PHE D:602 , CYS D:620 , VAL D:622 , CYS D:624 , PHE D:625 , ILE D:634 , CYS D:639 , ILE D:640 , CYS D:642 , ALA D:643 , CYS D:645	BINDING SITE FOR RESIDUE SF4 D 707
8	AC8	SOFTWARE	CYS D:608 , LYS D:612 , TYR D:613 , THR D:614 , ASP D:615 , CYS D:616 , CYS D:649 , ILE D:654	BINDING SITE FOR RESIDUE F3S D 708

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

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

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

Asymmetric Unit (2, 8)

	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.	FER1_AZOVI	31-60 1-30	4	A:30-59 B:230-259 C:430-459 D:630-659 -
2	4FE4S_FER_1	PS00198	4Fe-4S ferredoxin-type iron-sulfur binding region signature.	FER1_AZOVI	40-51	4	A:39-50 B:239-250 C:439-450 D:639-650

Biological Unit 1 (2, 2)

	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.	FER1_AZOVI	31-60 1-30	1	A:30-59 - - - -
2	4FE4S_FER_1	PS00198	4Fe-4S ferredoxin-type iron-sulfur binding region signature.	FER1_AZOVI	40-51	1	A:39-50 - - -

Biological Unit 2 (2, 2)

	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.	FER1_AZOVI	31-60 1-30	1	- B:230-259 - - -
2	4FE4S_FER_1	PS00198	4Fe-4S ferredoxin-type iron-sulfur binding region signature.	FER1_AZOVI	40-51	1	- B:239-250 - -

Biological Unit 3 (2, 2)

	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.	FER1_AZOVI	31-60 1-30	1	- - C:430-459 - -
2	4FE4S_FER_1	PS00198	4Fe-4S ferredoxin-type iron-sulfur binding region signature.	FER1_AZOVI	40-51	1	- - C:439-450 -

Biological Unit 4 (2, 2)

	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.	FER1_AZOVI	31-60 1-30	1	- - - D:630-659 -
2	4FE4S_FER_1	PS00198	4Fe-4S ferredoxin-type iron-sulfur binding region signature.	FER1_AZOVI	40-51	1	- - - D:639-650

(no "Exon" information available for 1GAO)

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:106
 aligned with FER1_AZOVI | P00214 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:106
                                    11        21        31        41        51        61        71        81        91       101      
           FER1_AZOVI     2 AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELAEVWPNITEKKDPLPDAEDWDGVKGKLQHLER 107
               SCOP domains d1gaoa_ A: Ferredoxin                                                                                      SCOP domains
               CATH domains 1gaoA00 A:1-106  [code=3.30.70.20, no name defined]                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhh.....hhhhh.....eee....eee.........hhhhhh....eee.hhhhhhhhhhhhhhhhhhh.............hhhhhh...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) 4FE4S_FER_2  PDB: -          4FE4S_FER_2  PDB: A:30-59     ----------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------4FE4S_FER_1 -------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1gao A   1 AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCASCEPECPAQAIFSEDEVPEDMQEFIQLNAELAEVWPNITEKKDPLPDAEDWDGVKGKLQHLER 106
                                    10        20        30        40        50        60        70        80        90       100

Chain B from PDB  Type:PROTEIN  Length:106
 aligned with FER1_AZOVI | P00214 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:106
                                    11        21        31        41        51        61        71        81        91       101      
           FER1_AZOVI     2 AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELAEVWPNITEKKDPLPDAEDWDGVKGKLQHLER 107
               SCOP domains d1gaob_ B: Ferredoxin                                                                                      SCOP domains
               CATH domains 1gaoB00 B:201-306  [code=3.30.70.20, no name defined]                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhh....hhhhhhh....eee....eee...................eee.hhhhhhhhhhhhhhhhhhh.............hhhhhh...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) 4FE4S_FER_2  PDB: -          4FE4S_FER_2  PDB: B:230-259   ----------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------4FE4S_FER_1 -------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1gao B 201 AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCASCEPECPAQAIFSEDEVPEDMQEFIQLNAELAEVWPNITEKKDPLPDAEDWDGVKGKLQHLER 306
                                   210       220       230       240       250       260       270       280       290       300

Chain C from PDB  Type:PROTEIN  Length:106
 aligned with FER1_AZOVI | P00214 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:106
                                    11        21        31        41        51        61        71        81        91       101      
           FER1_AZOVI     2 AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELAEVWPNITEKKDPLPDAEDWDGVKGKLQHLER 107
               SCOP domains d1gaoc_ C: Ferredoxin                                                                                      SCOP domains
               CATH domains 1gaoC00 C:401-506  [code=3.30.70.20, no name defined]                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhh....hhhhhhh....eee....eee.........hhhhhh....eee.hhhhhhhhhhhhhhhhhhhhh...........hhhhhh...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) 4FE4S_FER_2  PDB: -          4FE4S_FER_2  PDB: C:430-459   ----------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------4FE4S_FER_1 -------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1gao C 401 AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCASCEPECPAQAIFSEDEVPEDMQEFIQLNAELAEVWPNITEKKDPLPDAEDWDGVKGKLQHLER 506
                                   410       420       430       440       450       460       470       480       490       500

Chain D from PDB  Type:PROTEIN  Length:106
 aligned with FER1_AZOVI | P00214 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:106
                                    11        21        31        41        51        61        71        81        91       101      
           FER1_AZOVI     2 AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELAEVWPNITEKKDPLPDAEDWDGVKGKLQHLER 107
               SCOP domains d1gaod_ D: Ferredoxin                                                                                      SCOP domains
               CATH domains 1gaoD00 D:601-706  [code=3.30.70.20, no name defined]                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhh....hhhhhh.....eee....eee...................eee.hhhhhhhhhhhhhhhhhhhhh...........hhhhhh...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) 4FE4S_FER_2  PDB: -          4FE4S_FER_2  PDB: D:630-659   ----------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------4FE4S_FER_1 -------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1gao D 601 AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCASCEPECPAQAIFSEDEVPEDMQEFIQLNAELAEVWPNITEKKDPLPDAEDWDGVKGKLQHLER 706
                                   610       620       630       640       650       660       670       680       690       700

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

Fold: Ferredoxin-like (1795)

Superfamily: 4Fe-4S ferredoxins (143)

Family: 7-Fe ferredoxin (40)

Protein domain: Ferredoxin (37)

Azotobacter vinelandii [TaxId: 354] (32)

1a	d1gaoa_	A:
1b	d1gaob_	B:
1c	d1gaoc_	C:
1d	d1gaod_	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)

Azotobacter vinelandii. Organism_taxid: 354 (14)

1a	1gaoA00	A:1-106
1b	1gaoB00	B:201-306
1c	1gaoC00	C:401-506
1d	1gaoD00	D:601-706

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (FER1_AZOVI | P00214)

molecular function
	GO:0051538	3 iron, 4 sulfur cluster binding	Interacting selectively and non-covalently with a 3 iron, 4 sulfur (3Fe-4S) cluster; this cluster consists of three iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. It is essentially a 4Fe-4S cluster with one iron missing.
	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:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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.
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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7fd1	NATIVE FERREDOXIN I STRUCTURE

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