1ZT9 - JenaLib

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Biological Unit 5 (Jmol Viewer)

Title :   E. COLI TRP REPRESSOR, TETRAGONAL CRYSTAL FORM

Authors :   C. L. Lawson, A. S. Chin, B. Benoff, B. H. Yung

Date :   26 May 05 (Deposition) - 09 May 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,D,E
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: D,E  (1x)
Biol. Unit 3: A,B,D,E  (1x)
Biol. Unit 4: A (1x),B (1x),D (1x),E (1x)
Biol. Unit 5: A (1x),B (1x),D (1x),E (1x)

Keywords :   Helix-Turn-Helix, Dna-Binding Protein, Protein-Protein Interaction, L-Tryptophan Binding Protein, Bound Sulfate Anions, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. L. Lawson, A. S. Chin, B. Benoff, B. H. Yung
Two Association Modes For E. Coli Trp Repressor Dimer-Dimer Interactions
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - TRP OPERON REPRESSOR
	Chains	:	A, B, D, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET13ATRPR
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	TRPR, RTRY
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2	3	4
Asymmetric Unit	:	A	B	D	E
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			D	E
Biological Unit 3 (1x)	:	A	B	D	E
Biological Unit 4 (1x)	:	A (1x)	B (1x)	D (1x)	E (1x)
Biological Unit 5 (1x)	:	A (1x)	B (1x)	D (1x)	E (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 12)

No.	Name	Count	Type	Full Name
1	SO4	8	Ligand/Ion	SULFATE ION
2	TRP	4	Mod. Amino Acid	TRYPTOPHAN

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION
2	TRP	2	Mod. Amino Acid	TRYPTOPHAN

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION
2	TRP	2	Mod. Amino Acid	TRYPTOPHAN

Biological Unit 3 (2, 12)

No.	Name	Count	Type	Full Name
1	SO4	8	Ligand/Ion	SULFATE ION
2	TRP	4	Mod. Amino Acid	TRYPTOPHAN

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION
2	TRP	-1	Mod. Amino Acid	TRYPTOPHAN

Biological Unit 5 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION
2	TRP	-1	Mod. Amino Acid	TRYPTOPHAN

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR D:81 , ARG D:84 , TRP E:701	BINDING SITE FOR RESIDUE SO4 D 1
02	AC2	SOFTWARE	TRP D:801 , THR E:81 , ARG E:84 , HOH E:738 , HOH E:747	BINDING SITE FOR RESIDUE SO4 E 109
03	AC3	SOFTWARE	TRP A:1001 , HOH A:1128 , ARG B:54 , THR B:81 , ARG B:84 , HOH B:927	BINDING SITE FOR RESIDUE SO4 B 109
04	AC4	SOFTWARE	SER B:67 , GLN B:68 , HOH B:940	BINDING SITE FOR RESIDUE SO4 B 110
05	AC5	SOFTWARE	ARG D:69 , SER E:67 , GLN E:68 , HOH E:784 , HOH E:807	BINDING SITE FOR RESIDUE SO4 E 110
06	AC6	SOFTWARE	ARG A:54 , THR A:81 , ARG A:84 , HOH A:1127 , TRP B:901	BINDING SITE FOR RESIDUE SO4 A 109
07	AC7	SOFTWARE	SER D:67 , GLN D:68 , HOH D:878 , HOH D:933	BINDING SITE FOR RESIDUE SO4 D 109
08	AC8	SOFTWARE	SER A:67 , GLN A:68 , HOH A:1112	BINDING SITE FOR RESIDUE SO4 A 110
09	AC9	SOFTWARE	ARG A:54 , THR A:81 , GLY A:85 , SER A:88 , SO4 A:109 , HOH A:1011 , HOH A:1051 , ASN B:40 , LEU B:41 , LEU B:43 , THR B:44 , PRO B:45 , HOH B:967 , HOH B:977	BINDING SITE FOR RESIDUE TRP B 901
10	BC1	SOFTWARE	ASN A:40 , LEU A:41 , LEU A:43 , THR A:44 , PRO A:45 , HOH A:1034 , HOH A:1058 , ARG B:54 , THR B:81 , GLY B:85 , SER B:88 , SO4 B:109 , HOH B:925 , HOH B:939	BINDING SITE FOR RESIDUE TRP A 1001
11	BC2	SOFTWARE	SO4 D:1 , ARG D:54 , THR D:81 , GLY D:85 , SER D:88 , HOH D:821 , HOH D:828 , ASN E:40 , LEU E:41 , LEU E:43 , THR E:44 , PRO E:45 , HOH E:713 , HOH E:720	BINDING SITE FOR RESIDUE TRP E 701
12	BC3	SOFTWARE	ASN D:40 , LEU D:41 , LEU D:43 , THR D:44 , PRO D:45 , HOH D:811 , HOH D:835 , HOH D:851 , HOH D:857 , ARG E:54 , THR E:81 , GLY E:85 , SER E:88 , SO4 E:109 , HOH E:768	BINDING SITE FOR RESIDUE TRP D 801

(no "SS Bond" information available for 1ZT9)

(no "Cis Peptide Bond" information available for 1ZT9)

(no "SAP(SNP)/Variant" information available for 1ZT9)

(no "PROSITE Motif" information available for 1ZT9)

(no "Exon" information available for 1ZT9)

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:101
 aligned with TRPR_ECOLI | P0A881 from UniProtKB/Swiss-Prot  Length:108

    Alignment length:101
                                    14        24        34        44        54        64        74        84        94       104 
           TRPR_ECOLI     5 SPYSAAMAEQRHQEWLRFVDLLKNAYQNDLHLPLLNLMLTPDEREALGTRVRIVEELLRGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEEVLL 105
               SCOP domains d1zt9a_ A: Trp repressor, TrpR                                                                        SCOP domains
               CATH domains 1zt9A00 A:5-105 Trp Operon Repressor; Chain A                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 1zt9 A   5 SPYSAAMAEQRHQEWLRFVDLLKNAYQNDLHLPLLNLMLTPDEREALGTRVRIVEELLRGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEEVLL 105
                                    14        24        34        44        54        64        74        84        94       104

Chain B from PDB  Type:PROTEIN  Length:101
 aligned with TRPR_ECOLI | P0A881 from UniProtKB/Swiss-Prot  Length:108

    Alignment length:101
                                    14        24        34        44        54        64        74        84        94       104 
           TRPR_ECOLI     5 SPYSAAMAEQRHQEWLRFVDLLKNAYQNDLHLPLLNLMLTPDEREALGTRVRIVEELLRGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEEVLL 105
               SCOP domains d1zt9b_ B: Trp repressor, TrpR                                                                        SCOP domains
               CATH domains 1zt9B00 B:5-105 Trp Operon Repressor; Chain A                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 1zt9 B   5 SPYSAAMAEQRHQEWLRFVDLLKNAYQNDLHLPLLNLMLTPDEREALGTRVRIVEELLRGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEEVLL 105
                                    14        24        34        44        54        64        74        84        94       104

Chain D from PDB  Type:PROTEIN  Length:101
 aligned with TRPR_ECOLI | P0A881 from UniProtKB/Swiss-Prot  Length:108

    Alignment length:101
                                    14        24        34        44        54        64        74        84        94       104 
           TRPR_ECOLI     5 SPYSAAMAEQRHQEWLRFVDLLKNAYQNDLHLPLLNLMLTPDEREALGTRVRIVEELLRGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEEVLL 105
               SCOP domains d1zt9d_ D: Trp repressor, TrpR                                                                        SCOP domains
               CATH domains 1zt9D00 D:5-105 Trp Operon Repressor; Chain A                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 1zt9 D   5 SPYSAAMAEQRHQEWLRFVDLLKNAYQNDLHLPLLNLMLTPDEREALGTRVRIVEELLRGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEEVLL 105
                                    14        24        34        44        54        64        74        84        94       104

Chain E from PDB  Type:PROTEIN  Length:101
 aligned with TRPR_ECOLI | P0A881 from UniProtKB/Swiss-Prot  Length:108

    Alignment length:101
                                    14        24        34        44        54        64        74        84        94       104 
           TRPR_ECOLI     5 SPYSAAMAEQRHQEWLRFVDLLKNAYQNDLHLPLLNLMLTPDEREALGTRVRIVEELLRGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEEVLL 105
               SCOP domains d1zt9e_ E: Trp repressor, TrpR                                                                        SCOP domains
               CATH domains 1zt9E00 E:5-105 Trp Operon Repressor; Chain A                                                         CATH domains
           Pfam domains (1) ------------Trp_repressor-1zt9E01 E:17-104                                                          - Pfam domains (1)
           Pfam domains (2) ------------Trp_repressor-1zt9E02 E:17-104                                                          - Pfam domains (2)
           Pfam domains (3) ------------Trp_repressor-1zt9E03 E:17-104                                                          - Pfam domains (3)
           Pfam domains (4) ------------Trp_repressor-1zt9E04 E:17-104                                                          - Pfam domains (4)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 1zt9 E   5 SPYSAAMAEQRHQEWLRFVDLLKNAYQNDLHLPLLNLMLTPDEREALGTRVRIVEELLRGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEEVLL 105
                                    14        24        34        44        54        64        74        84        94       104

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: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: TrpR-like (20)

Family: Trp repressor, TrpR (15)

Protein domain: Trp repressor, TrpR (14)

Escherichia coli [TaxId: 562] (14)

1a	d1zt9a_	A:
1b	d1zt9b_	B:
1c	d1zt9d_	D:
1d	d1zt9e_	E:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Trp Operon Repressor; Chain A (18)

Homologous Superfamily: Trp Operon Repressor; Chain A (13)

Escherichia coli. Organism_taxid: 562. (4)

1a	1zt9A00	A:5-105
1b	1zt9B00	B:5-105
1c	1zt9D00	D:5-105
1d	1zt9E00	E:5-105

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: Trp_repressor (9)

Escherichia coli (strain K12) (8)

1a	Trp_repressor-1zt9E01	E:17-104
1b	Trp_repressor-1zt9E02	E:17-104
1c	Trp_repressor-1zt9E03	E:17-104
1d	Trp_repressor-1zt9E04	E:17-104

Asymmetric Unit(hide GO term definitions)

Chain A,B,D,E (TRPR_ECOLI | P0A881)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
	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.
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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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	1zt9
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	TRPR_ECOLI \| P0A881	:	1co0 1jhg 1mi7 1rcs 1tro 1trr 1wrp 1wrs 1wrt 2oz9 3ssw 3ssx 3wrp

1trr	E COLI TRP REPRESSOR/OPERATOR DNA TANDEM COMPLEX
1wrp	E COLI TRP REPRESSOR, TRIGONAL CRYSTAL FORM
2wrp	E COLI TRP REPRESSOR, ORTHORHOMBIC CRYSTAL FORM

Description

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Ligands, Modified Residues, Ions (2, 12)

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