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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   C-TERMINAL DOMAIN OF ESCHERICHIA COLI ARGININE REPRESSOR/ L-ARGININE COMPLEX

Authors :   G. D. Van Duyne, G. Ghosh, W. K. Maas, P. B. Sigler

Date :   03 Nov 95 (Deposition) - 08 Mar 96 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym./Biol. Unit : A,B,C,D,E,F

Keywords :   Complex (Dna Binding Protein-Peptide), Complex (Dna Binding Protein- Peptide) Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. D. Van Duyne, G. Ghosh, W. K. Maas, P. B. Sigler
Structure Of The Oligomerization And L-Arginine Binding Domain Of The Arginine Repressor Of Escherichia Coli.
J. Mol. Biol. V. 256 377 1996
PubMed-ID: 8594204 | Reference-DOI: 10.1006/JMBI.1996.0093
(for further references see the PDB file header)

Molecule 1 - ARGININE REPRESSOR
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Gene	:	T7
	Expression System Plasmid	:	PET3A
	Expression System Taxid	:	562
	Expression System Vector Type	:	T7
	Fragment	:	INITIATOR MET PLUS C-TERMINAL RESIDUES 80 - 156
	Gene	:	T7
	Organism Scientific	:	ESCHERICHIA COLI K12
	Organism Taxid	:	83333
	Other Details	:	T7 PROMOTER SYSTEM (NOVAGEN)
	Strain	:	K-12
	Synonym	:	ARGR

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 6)

No.	Name	Count	Type	Full Name
1	ARG	6	Mod. Amino Acid	ARGININE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:106 , ASP A:113 , THR A:124 , ILE A:125 , ALA A:126 , GLY C:127 , ASP C:128 , ASP C:129 , THR C:130 , ASP D:128	BINDING SITE FOR RESIDUE ARG A 1
2	AC2	SOFTWARE	GLY A:127 , ASP A:128 , ASP A:129 , THR A:130 , HOH A:158 , HOH A:175 , GLN B:106 , ALA B:109 , ASP B:113 , THR B:124 , ALA B:126 , ARG F:1 , PRO F:102 , ASP F:128	BINDING SITE FOR RESIDUE ARG A 157
3	AC3	SOFTWARE	GLY B:127 , ASP B:128 , ASP B:129 , THR B:130 , GLN C:106 , ALA C:109 , ASP C:113 , THR C:124 , ALA C:126 , ASP E:128 , ARG F:157	BINDING SITE FOR RESIDUE ARG C 1
4	AC4	SOFTWARE	PRO A:102 , GLY A:103 , ASP A:128 , ARG A:157 , GLN D:106 , ASP D:113 , THR D:124 , ALA D:126 , GLY F:127 , ASP F:128 , ASP F:129 , THR F:130	BINDING SITE FOR RESIDUE ARG F 1
5	AC5	SOFTWARE	ASP C:128 , GLY D:127 , ASP D:128 , ASP D:129 , THR D:130 , GLN E:106 , ALA E:109 , ASP E:113 , THR E:124 , ALA E:126 , HOH E:165	BINDING SITE FOR RESIDUE ARG E 1
6	AC6	SOFTWARE	GLY B:103 , ASP B:128 , ARG C:1 , GLY E:127 , ASP E:128 , ASP E:129 , THR E:130 , GLN F:106 , ALA F:109 , ARG F:110 , ASP F:113 , THR F:124 , ILE F:125 , ALA F:126	BINDING SITE FOR RESIDUE ARG F 157

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

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

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

(no "PROSITE Motif" information available for 1XXB)

(no "Exon" information available for 1XXB)

Asymmetric/Biological 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
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Chain A from PDB  Type:PROTEIN  Length:73
 aligned with ARGR_ECOLI | P0A6D0 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:74
                                    91       101       111       121       131       141       151    
           ARGR_ECOLI    82 LKNLVLDIDYNDAVVVIHTSPGAAQLIARLLDSLGKAEGILGTIAGDDTIFTTPANGFTVKDLYEAILELFDQE 155
               SCOP domains d1xxba_ A: C-terminal domain of arginine repressor                         SCOP domains
               CATH domains 1xxbA00 A:82-152  [code=3.30.1360.40, no name defined]                 --- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhh...eee....eeee.....hhhhhhhhhh..hhh.eeeeee...eeeeee.....hhhhhhhhhhh.-.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 1xxb A  82 LKNLVLDIDYNDAVVVIHTSPGAAQLIARLLDSLGKAEGILGTIAGDDTIFTTPANGFTVKDLYEAILELF-RR 157
                                    91       101       111       121       131       141       151| ||
                                                                                                152 1|
                                                                                                   157

Chain B from PDB  Type:PROTEIN  Length:72
 aligned with ARGR_ECOLI | P0A6D0 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:72
                                    90       100       110       120       130       140       150  
           ARGR_ECOLI    81 PLKNLVLDIDYNDAVVVIHTSPGAAQLIARLLDSLGKAEGILGTIAGDDTIFTTPANGFTVKDLYEAILELF 152
               SCOP domains d1xxbb_ B: C-terminal domain of arginine repressor                       SCOP domains
               CATH domains 1xxbB00 B:81-152  [code=3.30.1360.40, no name defined]                   CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhheeeeee....eeeee....hhhhhhhhh...hhh....eee...eeee.......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 1xxb B  81 PLKNLVLDIDYNDAVVVIHTSPGAAQLIARLLDSLGKAEGILGTIAGDDTIFTTPANGFTVKDLYEAILELF 152
                                    90       100       110       120       130       140       150

Chain C from PDB  Type:PROTEIN  Length:73
 aligned with ARGR_ECOLI | P0A6D0 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:74
                                    90       100       110       120       130       140       150    
           ARGR_ECOLI    81 PLKNLVLDIDYNDAVVVIHTSPGAAQLIARLLDSLGKAEGILGTIAGDDTIFTTPANGFTVKDLYEAILELFDQ 154
               SCOP domains d1xxbc_ C: C-terminal domain of arginine repressor                         SCOP domains
               CATH domains 1xxbC00 C:81-152  [code=3.30.1360.40, no name defined]                  -- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhheeeeee....eeeee....hhhhhhhhhh..hhh.eeeeee...eeeeee.....hhhhhhhhhhh.-. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 1xxb C  81 PLKNLVLDIDYNDAVVVIHTSPGAAQLIARLLDSLGKAEGILGTIAGDDTIFTTPANGFTVKDLYEAILELF-R   1
                                    90       100       110       120       130       140       150 | |
                                                                                                 152 1

Chain D from PDB  Type:PROTEIN  Length:71
 aligned with ARGR_ECOLI | P0A6D0 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:71
                                    91       101       111       121       131       141       151 
           ARGR_ECOLI    82 LKNLVLDIDYNDAVVVIHTSPGAAQLIARLLDSLGKAEGILGTIAGDDTIFTTPANGFTVKDLYEAILELF 152
               SCOP domains d1xxbd_ D: C-terminal domain of arginine repressor                      SCOP domains
               CATH domains 1xxbD00 D:82-152  [code=3.30.1360.40, no name defined]                  CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhh..........eeee....hhhhhhhhhhhh.hhh.eeeeee...eeeeee.....hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 1xxb D  82 LKNLVLDIDYNDAVVVIHTSPGAAQLIARLLDSLGKAEGILGTIAGDDTIFTTPANGFTVKDLYEAILELF 152
                                    91       101       111       121       131       141       151

Chain E from PDB  Type:PROTEIN  Length:72
 aligned with ARGR_ECOLI | P0A6D0 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:72
                                    91       101       111       121       131       141       151  
           ARGR_ECOLI    82 LKNLVLDIDYNDAVVVIHTSPGAAQLIARLLDSLGKAEGILGTIAGDDTIFTTPANGFTVKDLYEAILELFD 153
               SCOP domains d1xxbe_ E: C-terminal domain of arginine repressor                       SCOP domains
               CATH domains 1xxbE00 E:82-152  [code=3.30.1360.40, no name defined]                 - CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhheeeeee....eeeee....hhhhhhhhhh..hhh....eee...eeee.......hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 1xxb E  82 LKNLVLDIDYNDAVVVIHTSPGAAQLIARLLDSLGKAEGILGTIAGDDTIFTTPANGFTVKDLYEAILELFR   1
                                    91       101       111       121       131       141       151||
                                                                                                152|
                                                                                                   1

Chain F from PDB  Type:PROTEIN  Length:73
 aligned with ARGR_ECOLI | P0A6D0 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:73
                                    91       101       111       121       131       141       151   
           ARGR_ECOLI    82 LKNLVLDIDYNDAVVVIHTSPGAAQLIARLLDSLGKAEGILGTIAGDDTIFTTPANGFTVKDLYEAILELFDQ 154
               SCOP domains d1xxbf_ F: C-terminal domain of arginine repressor                        SCOP domains
               CATH domains 1xxbF00 F:82-152  [code=3.30.1360.40, no name defined]                 -- CATH domains
           Pfam domains (1) Arg_repressor_C-1xxbF01 F:82-151                                      --- Pfam domains (1)
           Pfam domains (2) Arg_repressor_C-1xxbF02 F:82-151                                      --- Pfam domains (2)
           Pfam domains (3) Arg_repressor_C-1xxbF03 F:82-151                                      --- Pfam domains (3)
           Pfam domains (4) Arg_repressor_C-1xxbF04 F:82-151                                      --- Pfam domains (4)
           Pfam domains (5) Arg_repressor_C-1xxbF05 F:82-151                                      --- Pfam domains (5)
           Pfam domains (6) Arg_repressor_C-1xxbF06 F:82-151                                      --- Pfam domains (6)
         Sec.struct. author ....eeee......eeeee....hhhhhhhhhh..hhh.eeeeee...eeeeee.....hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 1xxb F  82 LKNLVLDIDYNDAVVVIHTSPGAAQLIARLLDSLGKAEGILGTIAGDDTIFTTPANGFTVKDLYEAILELFRR 157
                                    91       101       111       121       131       141       151|||
                                                                                                152||
                                                                                                   1|
                                                                                                  157

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: DCoH-like (107)

Superfamily: C-terminal domain of arginine repressor (10)

Family: C-terminal domain of arginine repressor (7)

Protein domain: C-terminal domain of arginine repressor (7)

Escherichia coli [TaxId: 562] (3)

1a	d1xxba_	A:
1b	d1xxbe_	E:
1c	d1xxbf_	F:
1d	d1xxbb_	B:
1e	d1xxbc_	C:
1f	d1xxbd_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Gyrase A; domain 2 (166)

Homologous Superfamily: [code=3.30.1360.40, no name defined] (32)

Escherichia coli k12. Organism_taxid: 83333. Strain: k-12. (3)

1a	1xxbB00	B:81-152
1b	1xxbE00	E:82-152
1c	1xxbF00	F:82-152
1d	1xxbC00	C:81-152
1e	1xxbA00	A:82-152
1f	1xxbD00	D:82-152

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Arg_repressor_C] (6)

Family: Arg_repressor_C (6)

Escherichia coli (strain K12) (3)

1a	Arg_repressor_C-1xxbF01	F:82-151
1b	Arg_repressor_C-1xxbF02	F:82-151
1c	Arg_repressor_C-1xxbF03	F:82-151
1d	Arg_repressor_C-1xxbF04	F:82-151
1e	Arg_repressor_C-1xxbF05	F:82-151
1f	Arg_repressor_C-1xxbF06	F:82-151

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D,E,F (ARGR_ECOLI | P0A6D0)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0034618	arginine binding	Interacting selectively and non-covalently with 2-amino-5-(carbamimidamido)pentanoic acid.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0044212	transcription regulatory region DNA binding	Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
biological process
	GO:0006310	DNA recombination	Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
	GO:0006526	arginine biosynthetic process	The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
	GO:0006525	arginine metabolic process	The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:2000143	negative regulation of DNA-templated transcription, initiation	Any process that stops, prevents, or reduces the frequency, rate or extent of DNA-templated transcription initiation.
	GO:0042150	plasmid recombination	A process of DNA recombination occurring within a plasmid or between plasmids and other plasmids or DNA molecules.
	GO:0051259	protein oligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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Description

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