2RG1 - JenaLib

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Title :   CRYSTAL STRUCTURE OF E. COLI WRBA APOPROTEIN

Authors :   I. Kuta Smatanova, J. Wolfova, J. Brynda, M. Lapkouski, J. R. Mesters, R. Grandori, J. Carey

Date :   02 Oct 07 (Deposition) - 14 Oct 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Electron Transport, Quinone Oxidoreductase, Flavoprotein, Flavodoxin- Like Fold, Fmn-Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Wolfova, I. K. Smatanova, J. Brynda, J. R. Mesters, M. Lapkouski, M. Kuty, A. Natalello, N. Chatterjee, S. Y. Chern, E. Ebbel, A. Ricci, R. Grandori, R. Ettrich, J. Carey
Structural Organization Of Wrba In Apo- And Holoprotein Crystals.
Biochim. Biophys. Acta V. 1794 1288 2009
PubMed-ID: 19665595 | Reference-DOI: 10.1016/J.BBAPAP.2009.08.001

Molecule 1 - FLAVOPROTEIN WRBA
	Chains	:	A, B
	EC Number	:	1.6.5.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKGWA
	Expression System Strain	:	CY15071(LAMBDA-DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	WRBA
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	GENOMIC SEQUENCE CLONED IN PET3A
	Strain	:	K-12/JM101
	Synonym	:	TRP REPRESSOR-BINDING PROTEIN A

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:9 , MET A:10 , TYR A:11 , HIS A:13 , ILE A:14	BINDING SITE FOR RESIDUE CL A 200
2	AC2	SOFTWARE	SER B:9 , MET B:10 , TYR B:11 , HIS B:13 , ILE B:14	BINDING SITE FOR RESIDUE CL B 200

(no "SS Bond" information available for 2RG1)

Asymmetric Unit

No.	Residues
1	Gly A:156	-	Thr A:157

(no "SAP(SNP)/Variant" information available for 2RG1)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FLAVODOXIN_LIKE	PS50902	Flavodoxin-like domain profile.	NQOR_ECOLI	4-189	2	A:3-188 B:3-188

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FLAVODOXIN_LIKE	PS50902	Flavodoxin-like domain profile.	NQOR_ECOLI	4-189	4	A:3-188 B:3-188

(no "Exon" information available for 2RG1)

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:168
 aligned with NQOR_ECOLI | P0A8G6 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:196
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191      
           NQOR_ECOLI     2 AKVLVLYYSMYGHIETMARAVAEGASKVDGAEVVVKRVPETMPPQLFEKAGGKTQTAPVATPQELADYDAIIFGTPTRFGNMSGQMRTFLDQTGGLWASGALYGKLASVFSSTGTGGGQEQTITSTWTTLAHHGMVIVPIGYAAQELFDVSQVRGGTPYGATTIAGGDGSRQPSQEELSIARYQGEYVAGLAVKLN 197
               SCOP domains d2rg1a_ A: Trp repressor binding protein           WrbA                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhh....eeeeee....----------.........hhhhhhhh.eeeeeeeee..eehhhhhhhhhhhhhhhhh......eeeeeee..--.hhhhhhhhhhhhhhh...ee......------------......ee..----....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --FLAVODOXIN_LIKE  PDB: A:3-188 UniProt: 4-189                                                                                                                                              -------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rg1 A   1 AKVLVLYYSMYGHIETMARAVAEGASKVDGAEVVVKRVPET----------GKTQTAPVATPQELADYDAIIFGTPTRFGNMSGQMRTFLDQTGGLWASGALYGKLASVFSSTG--GGQEQTITSTWTTLAHHGMVIVPIGYA------------GTPYGATTIA----SRQPSQEELSIARYQGEYVAGLAVKLN 196
                                    10        20        30        40|        - |      60        70        80        90       100       110   |  |120       130       140  |      -     | 160    |  170       180       190      
                                                                   41         52                                                           114  |                       143          156      165  170                          
                                                                                                                                              117

Chain B from PDB  Type:PROTEIN  Length:166
 aligned with NQOR_ECOLI | P0A8G6 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:197
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       
           NQOR_ECOLI     2 AKVLVLYYSMYGHIETMARAVAEGASKVDGAEVVVKRVPETMPPQLFEKAGGKTQTAPVATPQELADYDAIIFGTPTRFGNMSGQMRTFLDQTGGLWASGALYGKLASVFSSTGTGGGQEQTITSTWTTLAHHGMVIVPIGYAAQELFDVSQVRGGTPYGATTIAGGDGSRQPSQEELSIARYQGEYVAGLAVKLNG 198
               SCOP domains d2rg1b_ B: Trp repressor binding protein              WrbA                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhh....eeeeee....-------------.......hhhhhhh.eeeeee.ee..eehhhhhhhhhhhhhhhhhh.....eeeeeee.....hhhhhhhhhhhhhhhh..ee......------------......ee..------..hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --FLAVODOXIN_LIKE  PDB: B:3-188 UniProt: 4-189                                                                                                                                              --------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rg1 B   1 AKVLVLYYSMYGHIETMARAVAEGASKVDGAEVVVKRVPET-------------QTAPVATPQELADYDAIIFGTPTRFGNMSGQMRTFLDQTGGLWASGALYGKLASVFSSTGTGGGQEQTITSTWTTLAHHGMVIVPIGYA------------GTPYGATTIA------QPSQEELSIARYQGEYVAGLAVKLNG 197
                                    10        20        30        40|        -    |   60        70        80        90       100       110       120       130       140  |      -     | 160    |    - |     180       190       
                                                                   41            55                                                                                     143          156      165    172

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) (23833)

Fold: Flavodoxin-like (1057)

Superfamily: Flavoproteins (208)

Family: WrbA-like (12)

Protein domain: Trp repressor binding protein WrbA (8)

Escherichia coli [TaxId: 562] (3)

1a	d2rg1a_	A:
1b	d2rg1b_	B:

(no "CATH Domain" information available for 2RG1)

(no "Pfam Domain" information available for 2RG1)

Asymmetric Unit(hide GO term definitions)

Chain A,B (NQOR_ECOLI | P0A8G6)

molecular function
	GO:0010181	FMN binding	Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
	GO:0003955	NAD(P)H dehydrogenase (quinone) activity	Catalysis of the reaction: NAD(P)H + H+ + a quinone = NAD(P)+ + a hydroquinone.
	GO:0050661	NADP binding	Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
	GO:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	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.
	GO:0006979	response to oxidative stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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	Sites
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	Cis Peptide Bonds
		Gly A:156 - Thr A:157	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2rg1
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	1.6.5.2
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UniProtKB/Swiss-Prot
	NQOR_ECOLI \| P0A8G6	:	2r96 2r97 3b6i 3b6j 3b6k 3b6m 3zho 4yqe 5f12

2r96	E. COLI WRBA IN COMPLEX WITH OXIDISED FMN, CRYSTAL FORM GROWN FROM 25% ETHYLENE GLYCOL
2r97	E. COLI WRBA IN COMPLEX WITH OXIDISED FMN, CRYSTAL FORM GROWN FROM 20% PEG 8000, 0.1M TRIS-HCL, PH 8.0

Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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Gene Ontology (13, 13)

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