3U7R - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   FERB - FLAVOENZYME NAD(P)H:(ACCEPTOR) OXIDOREDUCTASE (FERB) FROM PARACOCCUS DENITRIFICANS

Authors :   J. Marek, T. Klumpler, V. Sedlacek, I. Kucera

Date :   14 Oct 11 (Deposition) - 24 Oct 12 (Release) - 21 May 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Alpha/Beta Twisted Open-Sheet, Lavoprotein, Quinone Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Sedlacek, T. Klumpler, J. Marek, I. Kucera
The Structural And Functional Basis Of Catalysis Mediated B Nad(P)H:Acceptor Oxidoreductase (Ferb) Of Paracoccus Denitrificans.
Plos One V. 9 96262 2014
PubMed-ID: 24817153 | Reference-DOI: 10.1371/JOURNAL.PONE.0096262

Molecule 1 - NADPH-DEPENDENT FMN REDUCTASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	BL21(DE3) PLYSS
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	FERB, PDEN_4071
	Organism Scientific	:	PARACOCCUS DENITRIFICANS
	Organism Taxid	:	318586
	Strain	:	PD1222

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 15)

No.	Name	Count	Type	Full Name
1	2PE	1	Ligand/Ion	NONAETHYLENE GLYCOL
2	FNR	2	Ligand/Ion	1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL
3	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (3, 15)

No.	Name	Count	Type	Full Name
1	2PE	1	Ligand/Ion	NONAETHYLENE GLYCOL
2	FNR	2	Ligand/Ion	1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL
3	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (3, 30)

No.	Name	Count	Type	Full Name
1	2PE	2	Ligand/Ion	NONAETHYLENE GLYCOL
2	FNR	4	Ligand/Ion	1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL
3	MSE	24	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:11 , ARG A:13 , SER A:16 , LEU A:17 , ASN A:18 , PRO A:76 , GLU A:77 , TYR A:78 , ASN A:79 , ARG A:80 , SER A:113 , PRO A:114 , HOH A:305 , HOH A:307 , HOH A:314 , HOH A:321 , HOH A:329 , HOH A:379 , HOH A:396 , TYR B:46 , THR B:94 , ARG B:95	BINDING SITE FOR RESIDUE FNR A 201
2	AC2	SOFTWARE	ASP A:42 , LEU A:43 , PRO A:44 , HIS A:45 , LEU A:50 , HOH A:429 , HOH A:501 , HOH A:524 , GLY B:41 , ASP B:42 , LEU B:43 , HIS B:45 , HOH B:463	BINDING SITE FOR RESIDUE 2PE A 202
3	AC3	SOFTWARE	TYR A:46 , ASP A:48 , ARG A:95 , SER B:11 , ARG B:13 , SER B:16 , LEU B:17 , ASN B:18 , PRO B:76 , GLU B:77 , TYR B:78 , ASN B:79 , ARG B:80 , SER B:113 , PRO B:114 , HOH B:305 , HOH B:316 , HOH B:320 , HOH B:330 , HOH B:331 , HOH B:333 , HOH B:396	BINDING SITE FOR RESIDUE FNR B 201

(no "SS Bond" information available for 3U7R)

Asymmetric Unit

No.	Residues
1	Arg A:95	-	Pro A:96
2	Mse A:140	-	Pro A:141
3	Arg B:95	-	Pro B:96
4	Mse B:140	-	Pro B:141

(no "SAP(SNP)/Variant" information available for 3U7R)

(no "PROSITE Motif" information available for 3U7R)

(no "Exon" information available for 3U7R)

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:182
 aligned with A1B9E3_PARDP | A1B9E3 from UniProtKB/TrEMBL  Length:182

    Alignment length:182
                                                                                                                                                                                                              182 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181| 
         A1B9E3_PARDP     2 VKTVAVMVGSLRKDSLNHKLMKVLQKLAEGRLEFHLLHIGDLPHYNDDLWADAPESVLRLKDRIEHSDAVLAITPEYNRSYPGMIKNAIDWATRPYGQNSWKGKPAAVIGTSPGVIGAALAQARLKNDLLHVGTVMMSMPEAYIQWHAEAYAADGSVTDEKTAKFLQGFVDAFVDWIEKHG-   -
               SCOP domains d3u7ra_ A: automated matches                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......hhhhhhhhhhhhhhh..eeeee.hhhhh...hhhhhhhhhhhhhhhhhhhhh..eeeee........hhhhhhhhhhhhh..........eeeeeeee.....hhhhhhhhhhhhhh...ee......eee.hhhhh.......hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u7r A   2 VKTVAVmVGSLRKDSLNHKLmKVLQKLAEGRLEFHLLHIGDLPHYNDDLWADAPESVLRLKDRIEHSDAVLAITPEYNRSYPGmIKNAIDWATRPYGQNSWKGKPAAVIGTSPGVIGAALAQARLKNDLLHVGTVmmSmPEAYIQWHAEAYAADGSVTDEKTAKFLQGFVDAFVDWIEKHGL 183
                                  | 11        21|       31        41        51        61        71        81   |    91       101       111       121       131     ||141       151       161       171       181  
                                  8-MSE        22-MSE                                                         85-MSE                                             137-MSE                                          
                                                                                                                                                                  138-MSE                                         
                                                                                                                                                                    140-MSE

Chain B from PDB  Type:PROTEIN  Length:182
 aligned with A1B9E3_PARDP | A1B9E3 from UniProtKB/TrEMBL  Length:182

    Alignment length:182
                                                                                                                                                                                                              182 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181| 
         A1B9E3_PARDP     2 VKTVAVMVGSLRKDSLNHKLMKVLQKLAEGRLEFHLLHIGDLPHYNDDLWADAPESVLRLKDRIEHSDAVLAITPEYNRSYPGMIKNAIDWATRPYGQNSWKGKPAAVIGTSPGVIGAALAQARLKNDLLHVGTVMMSMPEAYIQWHAEAYAADGSVTDEKTAKFLQGFVDAFVDWIEKHG-   -
               SCOP domains d3u7rb_ B: automated matches                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......hhhhhhhhhhhhhhh..eeeee.hhhhh...hhhhhhhhhhhhhhhhhhhhh..eeeee........hhhhhhhhhhhhh..........eeeeeeee.....hhhhhhhhhhhhhh...ee......eee.hhhhh.......hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u7r B   2 VKTVAVmVGSLRKDSLNHKLmKVLQKLAEGRLEFHLLHIGDLPHYNDDLWADAPESVLRLKDRIEHSDAVLAITPEYNRSYPGmIKNAIDWATRPYGQNSWKGKPAAVIGTSPGVIGAALAQARLKNDLLHVGTVmmSmPEAYIQWHAEAYAADGSVTDEKTAKFLQGFVDAFVDWIEKHGL 183
                                  | 11        21|       31        41        51        61        71        81   |    91       101       111       121       131     ||141       151       161       171       181  
                                  8-MSE        22-MSE                                                         85-MSE                                             137-MSE                                          
                                                                                                                                                                  138-MSE                                         
                                                                                                                                                                    140-MSE

Legend:		→ Mismatch	(orange background)
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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(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Flavodoxin-like (1057)

Superfamily: Flavoproteins (208)

Family: automated matches (29)

Protein domain: automated matches (29)

Paracoccus denitrificans [TaxId: 318586] (1)

1a	d3u7ra_	A:
1b	d3u7rb_	B:

(no "CATH Domain" information available for 3U7R)

(no "Pfam Domain" information available for 3U7R)

Asymmetric Unit(hide GO term definitions)

Chain A,B (A1B9E3_PARDP | A1B9E3)

molecular function
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
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
		Arg A:95 - Pro A:96	[ RasMol ]
		Arg B:95 - Pro B:96	[ RasMol ]
		Mse A:140 - Pro A:141	[ RasMol ]
		Mse B:140 - Pro B:141	[ RasMol ]

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		Biological Unit 2	[ Jena3D ]

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Description

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Ligands, Modified Residues, Ions (3, 15)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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