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Biological Unit 4 (Jmol Viewer)

Title :   STRUCTURE OF OXIDIZED C73S PUTIDAREDOXIN FROM PSEUDOMONAS PUTIDA

Authors :   I. F. Sevrioukova

Date :   30 Sep 04 (Deposition) - 04 Oct 05 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: B (1x),C (1x)

Keywords :   [2Fe-2S], Ferredoxin, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. F. Sevrioukova
Redox-Dependent Structural Reorganization In Putidaredoxin, A Vertebrate-Type [2Fe-2S] Ferredoxin From Pseudomonas Putida.
J. Mol. Biol. V. 347 607 2005
PubMed-ID: 15755454 | Reference-DOI: 10.1016/J.JMB.2005.01.047

Molecule 1 - PUTIDAREDOXIN
	Chains	:	A, B, C
	EC Number	:	1.9.3.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	CAMB
	Mutation	:	YES
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	303
	Synonym	:	PDX

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:		B (1x)	C (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	FES	3	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER

Biological Unit 1 (1, 1)

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

Biological Unit 2 (1, 1)

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

Biological Unit 3 (1, 1)

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

Biological Unit 4 (1, 1)

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

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:37 , CYS A:39 , GLY A:41 , ALA A:43 , SER A:44 , CYS A:45 , CYS A:48 , LEU A:84 , CYS A:86	BINDING SITE FOR RESIDUE FES A 107
2	AC2	SOFTWARE	GLY B:37 , CYS B:39 , GLY B:41 , ALA B:43 , CYS B:45 , CYS B:48 , CYS B:86	BINDING SITE FOR RESIDUE FES B 107
3	AC3	SOFTWARE	GLY C:37 , CYS C:39 , GLY C:41 , ALA C:43 , CYS C:45 , CYS C:48 , CYS C:86	BINDING SITE FOR RESIDUE FES C 107

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

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

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

Asymmetric Unit (2, 6)

	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.	PUTX_PSEPU	2-106	3	A:1-105 B:1-105 C:1-105
2	ADX	PS00814	Adrenodoxin family, iron-sulfur binding region signature.	PUTX_PSEPU	40-50	3	A:39-49 B:39-49 C:39-49

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.	PUTX_PSEPU	2-106	1	A:1-105 - -
2	ADX	PS00814	Adrenodoxin family, iron-sulfur binding region signature.	PUTX_PSEPU	40-50	1	A:39-49 - -

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.	PUTX_PSEPU	2-106	1	- B:1-105 -
2	ADX	PS00814	Adrenodoxin family, iron-sulfur binding region signature.	PUTX_PSEPU	40-50	1	- B:39-49 -

Biological Unit 3 (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.	PUTX_PSEPU	2-106	1	- - C:1-105
2	ADX	PS00814	Adrenodoxin family, iron-sulfur binding region signature.	PUTX_PSEPU	40-50	1	- - C:39-49

Biological Unit 4 (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.	PUTX_PSEPU	2-106	2	- B:1-105 C:1-105
2	ADX	PS00814	Adrenodoxin family, iron-sulfur binding region signature.	PUTX_PSEPU	40-50	2	- B:39-49 C:39-49

(no "Exon" information available for 1XLP)

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 PUTX_PSEPU | P00259 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:106
                                    11        21        31        41        51        61        71        81        91       101      
           PUTX_PSEPU     2 SKVVYVSHDGTRRELDVADGVSLMQAAVSNGIYDIVGDCGGSASCATCHVYVNEAFTDKVPAANEREIGMLECVTAELKPNSRLCCQIIMTPELDGIVVDVPDRQW 107
               SCOP domains d1xlpa_ A: 2Fe-2S ferredoxin                                                                               SCOP domains
               CATH domains 1xlpA00 A:1-106  [code=3.10.20.30, no name defined]                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhh...................eeee...........hhhhhhhhh.........eee.hhh..hhhhh.eeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) 2FE2S_FER_2  PDB: A:1-105 UniProt: 2-106                                                                 - PROSITE (1)
                PROSITE (2) --------------------------------------ADX        --------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1xlp A   1 SKVVYVSHDGTRRELDVADGVSLMQAAVSNGIYDIVGDCGGSASCATCHVYVNEAFTDKVPAANEREIGMLESVTAELKPNSRLCCQIIMTPELDGIVVDVPDRQW 106
                                    10        20        30        40        50        60        70        80        90       100

Chain B from PDB  Type:PROTEIN  Length:106
 aligned with PUTX_PSEPU | P00259 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:106
                                    11        21        31        41        51        61        71        81        91       101      
           PUTX_PSEPU     2 SKVVYVSHDGTRRELDVADGVSLMQAAVSNGIYDIVGDCGGSASCATCHVYVNEAFTDKVPAANEREIGMLECVTAELKPNSRLCCQIIMTPELDGIVVDVPDRQW 107
               SCOP domains d1xlpb_ B: 2Fe-2S ferredoxin                                                                               SCOP domains
               CATH domains 1xlpB00 B:1-106  [code=3.10.20.30, no name defined]                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhh..................eeee...hhhhh...hhhhhhhhh.........eee......hhhhh.eeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) 2FE2S_FER_2  PDB: B:1-105 UniProt: 2-106                                                                 - PROSITE (1)
                PROSITE (2) --------------------------------------ADX        --------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1xlp B   1 SKVVYVSHDGTRRELDVADGVSLMQAAVSNGIYDIVGDCGGSASCATCHVYVNEAFTDKVPAANEREIGMLESVTAELKPNSRLCCQIIMTPELDGIVVDVPDRQW 106
                                    10        20        30        40        50        60        70        80        90       100

Chain C from PDB  Type:PROTEIN  Length:106
 aligned with PUTX_PSEPU | P00259 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:106
                                    11        21        31        41        51        61        71        81        91       101      
           PUTX_PSEPU     2 SKVVYVSHDGTRRELDVADGVSLMQAAVSNGIYDIVGDCGGSASCATCHVYVNEAFTDKVPAANEREIGMLECVTAELKPNSRLCCQIIMTPELDGIVVDVPDRQW 107
               SCOP domains d1xlpc_ C: 2Fe-2S ferredoxin                                                                               SCOP domains
               CATH domains 1xlpC00 C:1-106  [code=3.10.20.30, no name defined]                                                        CATH domains
           Pfam domains (1) -----Fer2-1xlpC01 C:6-91                                                                   --------------- Pfam domains (1)
           Pfam domains (2) -----Fer2-1xlpC02 C:6-91                                                                   --------------- Pfam domains (2)
           Pfam domains (3) -----Fer2-1xlpC03 C:6-91                                                                   --------------- Pfam domains (3)
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhh..................eeee...hhhhh...hhhhhhhhh.........eee......hhhhh.eeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) 2FE2S_FER_2  PDB: C:1-105 UniProt: 2-106                                                                 - PROSITE (1)
                PROSITE (2) --------------------------------------ADX        --------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1xlp C   1 SKVVYVSHDGTRRELDVADGVSLMQAAVSNGIYDIVGDCGGSASCATCHVYVNEAFTDKVPAANEREIGMLESVTAELKPNSRLCCQIIMTPELDGIVVDVPDRQW 106
                                    10        20        30        40        50        60        70        80        90       100

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

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

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

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

Pseudomonas putida, putidaredoxin [TaxId: 303] (18)

1a	d1xlpa_	A:
1b	d1xlpb_	B:
1c	d1xlpc_	C:

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)

Pseudomonas putida. Organism_taxid: 303. (10)

1a	1xlpA00	A:1-106
1b	1xlpB00	B:1-106
1c	1xlpC00	C:1-106

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Fer2 (69)

Family: Fer2 (60)

Pseudomonas putida (Arthrobacter siderocapsulatus) (9)

1a	Fer2-1xlpC01	C:6-91
1b	Fer2-1xlpC02	C:6-91
1c	Fer2-1xlpC03	C:6-91

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (PUTX_PSEPU | P00259)

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.
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.

Asymmetric Unit
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	Cis Peptide Bonds
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Biological Units
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Access by PDB/NDB ID
	1xlp
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
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1oqr	STRUCTURE OF THE SAME PROTEIN SOLVED USING SYNCHROTRON RADIATION

Description

Compounds

Structural Features

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Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

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