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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF A 1.6-HEXANEDIOL BOUND TETRAMERIC FORM OF ESCHERICHIA COLI LAC-REPRESSOR REFINED TO 2.1 RESOLUTION

Authors :   K. A. E. Stenberg

Date :   03 Sep 08 (Deposition) - 25 Nov 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Lac-Repressor, Allosteric, Tetramer, Dna-Binding, Repressor, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. A. E. Stenberg, M. Vihinen
Crystal Structure Of A 1. 6-Hexanediol Bound Tetrameric Form Of Escherichia Coli Lac-Repressor Refined To 2. 1 A Resolution
Proteins V. 75 748 2009
PubMed-ID: 19004002 | Reference-DOI: 10.1002/PROT.22284

Molecule 1 - LACTOSE OPERON REPRESSOR
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Organism Scientific	:	ESCHERICHIA COLI K12
	Organism Taxid	:	83333

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	HEZ	4	Ligand/Ion	HEXANE-1,6-DIOL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:69 , LEU A:71 , PRO A:127 , TRP A:220 , HOH A:408 , HOH A:411 , HOH A:536 , HOH A:567	BINDING SITE FOR RESIDUE HEZ A 400
2	AC2	SOFTWARE	SER B:69 , TRP B:220 , ASN B:246 , ASP B:274 , HOH B:468 , HOH B:480 , HOH B:536 , HOH B:565	BINDING SITE FOR RESIDUE HEZ B 400
3	AC3	SOFTWARE	LEU C:73 , TRP C:220 , ASN C:246 , ASP C:274 , HOH C:442 , HOH C:482 , HOH C:493 , HOH C:552	BINDING SITE FOR RESIDUE HEZ C 400
4	AC4	SOFTWARE	SER D:69 , LEU D:73 , ASP D:149 , TRP D:220 , HOH D:520 , HOH D:557	BINDING SITE FOR RESIDUE HEZ D 400

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

Asymmetric/Biological Unit

No.	Residues
1	Ile A:283	-	Pro A:284
2	Ile B:283	-	Pro B:284
3	Ile C:283	-	Pro C:284
4	Ile D:283	-	Pro D:284

Asymmetric/Biological Unit (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LACI_ECOLI_001 *	Y	282	D	LACI_ECOLI	---	---	A/B/C/D	Y	282	D
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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

(no "Exon" information available for 3EDC)

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
	(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:300
 aligned with LACI_ECOLI | P03023 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:300
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360
           LACI_ECOLI    61 SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRLESGQ 360
               SCOP domains d3edca_ A: automated matches                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 3edcA01 A:61-161,A:291-320  [code=3.40.50.2300, no name defined]                                     3edcA02 A:162-290,A:321-336  [code=3.40.50.2300, no name defined]                                                                3edcA01 A:61-161,A:291-320    3edcA02         ------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh....eee..........eeeehhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhh........eeeeee.hhhhhhh....eeee.hhhhhhhhhhhhhhhhhh......eeee..eee.............hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3edc A  61 SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRLESGQ 360
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360

Chain B from PDB  Type:PROTEIN  Length:300
 aligned with LACI_ECOLI | P03023 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:300
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360
           LACI_ECOLI    61 SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRLESGQ 360
               SCOP domains d3edcb_ B: automated matches                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 3edcB01 B:61-161,B:291-320  [code=3.40.50.2300, no name defined]                                     3edcB02 B:162-290,B:321-336  [code=3.40.50.2300, no name defined]                                                                3edcB01 B:61-161,B:291-320    3edcB02         ------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh....eee..........eeeehhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhh........eeeeee.hhhhhhh....eeee.hhhhhhhhhhhhhhhhhh......eeee..eee.............hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3edc B  61 SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRLESGQ 360
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360

Chain C from PDB  Type:PROTEIN  Length:300
 aligned with LACI_ECOLI | P03023 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:300
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360
           LACI_ECOLI    61 SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRLESGQ 360
               SCOP domains d3edcc_ C: automated matches                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 3edcC01 C:61-161,C:291-320  [code=3.40.50.2300, no name defined]                                     3edcC02 C:162-290,C:321-336  [code=3.40.50.2300, no name defined]                                                                3edcC01 C:61-161,C:291-320    3edcC02         ------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh....eee..........eeeehhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhh........eee....hhhhhhh.....eee.hhhhhhhhhhhhhhhhhh......eeee..eee.............hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3edc C  61 SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRLESGQ 360
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360

Chain D from PDB  Type:PROTEIN  Length:300
 aligned with LACI_ECOLI | P03023 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:300
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360
           LACI_ECOLI    61 SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRLESGQ 360
               SCOP domains d3edcd_ D: automated matches                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 3edcD01 D:61-161,D:291-320  [code=3.40.50.2300, no name defined]                                     3edcD02 D:162-290,D:321-336  [code=3.40.50.2300, no name defined]                                                                3edcD01 D:61-161,D:291-320    3edcD02         ------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh....eee..........eeeehhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhh........eeeeee.hhhhhhh....eeee.hhhhhhhhhhhhhhhhhh......eeee..eee.............hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3edc D  61 SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRLESGQ 360
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360

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) (23833)

Fold: Periplasmic binding protein-like I (179)

Superfamily: Periplasmic binding protein-like I (179)

Family: L-arabinose binding protein-like (114)

Protein domain: automated matches (12)

Escherichia coli K-12 [TaxId: 83333] (6)

1a	d3edca_	A:
1b	d3edcb_	B:
1c	d3edcc_	C:
1d	d3edcd_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.2300, no name defined] (308)

Escherichia coli k12. Organism_taxid: 83333. (1)

1a	3edcA02	A:162-290,A:321-336
1b	3edcB02	B:162-290,B:321-336
1c	3edcC02	C:162-290,C:321-336
1d	3edcD02	D:162-290,D:321-336
1e	3edcA01	A:61-161,A:291-320
1f	3edcB01	B:61-161,B:291-320
1g	3edcC01	C:61-161,C:291-320
1h	3edcD01	D:61-161,D:291-320

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (LACI_ECOLI | P03023)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000986	bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase.
	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:0001141	transcriptional repressor activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase in order to stop, prevent, or reduce the frequency, rate or extent of transcription from a bacterial-type RNA polymerase promoter.
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: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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ile A:283 - Pro A:284	[ RasMol ]
		Ile B:283 - Pro B:284	[ RasMol ]
		Ile C:283 - Pro C:284	[ RasMol ]
		Ile D:283 - Pro D:284	[ RasMol ]

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	3edc
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Description

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Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

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