1Z9C | PD0644 - JenaLib

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Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF OHRR BOUND TO THE OHRA PROMOTER: STRUCTURE OF MARR FAMILY PROTEIN WITH OPERATOR DNA

Authors :   M. Hong, M. Fuangthong, J. D. Helmann, R. G. Brennan

Date :   01 Apr 05 (Deposition) - 25 Oct 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.64

Chains :   Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,G,H  (1x)
Biol. Unit 2: C,D,I,J  (1x)
Biol. Unit 3: E,F,K,L  (1x)

Keywords :   Ohrr, Marr Family Protein, Bacterial Transcription Factor, Winged Hth Protein, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Hong, M. Fuangthong, J. D. Helmann, R. G. Brennan
Structure Of An Ohrr-Ohra Operator Complex Reveals The Dna Binding Mechanism Of The Marr Family.
Mol. Cell V. 20 131 2005
PubMed-ID: 16209951 | Reference-DOI: 10.1016/J.MOLCEL.2005.09.013
(for further references see the PDB file header)

Molecule 1 - DNA (29-MER)
	Chains	:	G, I, K
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - DNA (29-MER)
	Chains	:	H, J, L
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - ORGANIC HYDROPEROXIDE RESISTANCE TRANSCRIPTIONAL REGULATOR
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET16X
	Expression System Strain	:	BL21(DE3)/PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	OHRR
	Mutation	:	YES
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

		1	2	3	4	5	6	7	8	9	10	11	12
Asymmetric Unit	:	A	B	C	D	E	F	G	H	I	J	K	L
Biological Unit 1 (1x)	:	A	B					G	H
Biological Unit 2 (1x)	:			C	D					I	J
Biological Unit 3 (1x)	:					E	F					K	L

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1Z9C)

(no "Site" information available for 1Z9C)

(no "SS Bond" information available for 1Z9C)

(no "Cis Peptide Bond" information available for 1Z9C)

(no "SAP(SNP)/Variant" information available for 1Z9C)

Asymmetric Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_MARR_2	PS50995	MarR-type HTH domain profile.	OHRR_BACSU	11-141	6	A:11-141 B:11-141 C:11-141 D:11-141 E:11-141 F:11-141

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_MARR_2	PS50995	MarR-type HTH domain profile.	OHRR_BACSU	11-141	2	A:11-141 B:11-141 - - - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_MARR_2	PS50995	MarR-type HTH domain profile.	OHRR_BACSU	11-141	2	- - C:11-141 D:11-141 - -

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_MARR_2	PS50995	MarR-type HTH domain profile.	OHRR_BACSU	11-141	2	- - - - E:11-141 F:11-141

(no "Exon" information available for 1Z9C)

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:137
 aligned with OHRR_BACSU | O34777 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:137
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       
           OHRR_BACSU     9 KLENQLCFLLYASSREMTKQYKPLLDKLNITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKEKAVDIPGTILGLSKQSGEDLKQLKSALYTLLETLHQ 145
               SCOP domains d1z9ca_ A: Organic hydroperoxide resistance transcriptional regulator OhrR                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...eeehhhhhhhhh.hhhhhhhhhhhhhhh..eeeee.......eeeeehhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --HTH_MARR_2  PDB: A:11-141 UniProt: 11-141                                                                                          ---- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z9c A   9 KLENQLSFLLYASSREMTKQYKPLLDKLNITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKEKAVDIPGTILGLSKQSGEDLKQLKSALYTLLETLHQ 145
                                    18        28        38        48        58        68        78        88        98       108       118       128       138

Chain B from PDB  Type:PROTEIN  Length:137
 aligned with OHRR_BACSU | O34777 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:137
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       
           OHRR_BACSU     8 MKLENQLCFLLYASSREMTKQYKPLLDKLNITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKEKAVDIPGTILGLSKQSGEDLKQLKSALYTLLETLH 144
               SCOP domains d1z9cb_ B: Organic hydroperoxide resistance transcriptional regulator OhrR                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh..eeehhhhhhhhh....hhhhhhhhhhhh..eeeee.......eeeeehhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---HTH_MARR_2  PDB: B:11-141 UniProt: 11-141                                                                                          --- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z9c B   8 MKLENQLSFLLYASSREMTKQYKPLLDKLNITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKEKAVDIPGTILGLSKQSGEDLKQLKSALYTLLETLH 144
                                    17        27        37        47        57        67        77        87        97       107       117       127       137

Chain C from PDB  Type:PROTEIN  Length:138
 aligned with OHRR_BACSU | O34777 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:138
                                    16        26        36        46        56        66        76        86        96       106       116       126       136        
           OHRR_BACSU     7 HMKLENQLCFLLYASSREMTKQYKPLLDKLNITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKEKAVDIPGTILGLSKQSGEDLKQLKSALYTLLETLH 144
               SCOP domains d1z9cc_ C: Organic hydroperoxide resistance transcriptional regulator OhrR                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...eeehhhhhhhhh.hhhhhhhhhhhhhhh..eeeee.......eeeeehhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----HTH_MARR_2  PDB: C:11-141 UniProt: 11-141                                                                                          --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1z9c C   7 HMKLENQLSFLLYASSREMTKQYKPLLDKLNITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKEKAVDIPGTILGLSKQSGEDLKQLKSALYTLLETLH 144
                                    16        26        36        46        56        66        76        86        96       106       116       126       136

Chain D from PDB  Type:PROTEIN  Length:137
 aligned with OHRR_BACSU | O34777 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:137
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       
           OHRR_BACSU     8 MKLENQLCFLLYASSREMTKQYKPLLDKLNITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKEKAVDIPGTILGLSKQSGEDLKQLKSALYTLLETLH 144
               SCOP domains d1z9cd_ D: Organic hydroperoxide resistance transcriptional regulator OhrR                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh...eeehhhhhhhh.....hhhhhhhhhhhh..eeeee.......eeeeehhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---HTH_MARR_2  PDB: D:11-141 UniProt: 11-141                                                                                          --- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z9c D   8 MKLENQLSFLLYASSREMTKQYKPLLDKLNITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKEKAVDIPGTILGLSKQSGEDLKQLKSALYTLLETLH 144
                                    17        27        37        47        57        67        77        87        97       107       117       127       137

Chain E from PDB  Type:PROTEIN  Length:137
 aligned with OHRR_BACSU | O34777 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:137
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       
           OHRR_BACSU     8 MKLENQLCFLLYASSREMTKQYKPLLDKLNITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKEKAVDIPGTILGLSKQSGEDLKQLKSALYTLLETLH 144
               SCOP domains d1z9ce_ E: Organic hydroperoxide resistance transcriptional regulator OhrR                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.eeehhhhhhhhh.hhhhhhhhhhhhhhh..eeeee.......eeeeehhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---HTH_MARR_2  PDB: E:11-141 UniProt: 11-141                                                                                          --- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z9c E   8 MKLENQLSFLLYASSREMTKQYKPLLDKLNITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKEKAVDIPGTILGLSKQSGEDLKQLKSALYTLLETLH 144
                                    17        27        37        47        57        67        77        87        97       107       117       127       137

Chain F from PDB  Type:PROTEIN  Length:138
 aligned with OHRR_BACSU | O34777 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:138
                                    16        26        36        46        56        66        76        86        96       106       116       126       136        
           OHRR_BACSU     7 HMKLENQLCFLLYASSREMTKQYKPLLDKLNITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKEKAVDIPGTILGLSKQSGEDLKQLKSALYTLLETLH 144
               SCOP domains d1z9cf_ F: Organic hydroperoxide resistance transcriptional regulator OhrR                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -------------------------------MarR-1z9cF01 F:38-96                                       ------------------------------------------------ Pfam domains (1)
           Pfam domains (2) -------------------------------MarR-1z9cF02 F:38-96                                       ------------------------------------------------ Pfam domains (2)
           Pfam domains (3) -------------------------------MarR-1z9cF03 F:38-96                                       ------------------------------------------------ Pfam domains (3)
           Pfam domains (4) -------------------------------MarR-1z9cF04 F:38-96                                       ------------------------------------------------ Pfam domains (4)
           Pfam domains (5) -------------------------------MarR-1z9cF05 F:38-96                                       ------------------------------------------------ Pfam domains (5)
           Pfam domains (6) -------------------------------MarR-1z9cF06 F:38-96                                       ------------------------------------------------ Pfam domains (6)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.eeehhhhhhhhh....hhhhhhhhhhhh..eeeee.......eeeeehhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----HTH_MARR_2  PDB: F:11-141 UniProt: 11-141                                                                                          --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1z9c F   7 HMKLENQLSFLLYASSREMTKQYKPLLDKLNITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKEKAVDIPGTILGLSKQSGEDLKQLKSALYTLLETLH 144
                                    16        26        36        46        56        66        76        86        96       106       116       126       136

Chain G from PDB  Type:DNA  Length:29
                                                             
                 1z9c G   1 TACAATTTAATTGTATACAATTTAATTGT  29
                                    10        20

Chain H from PDB  Type:DNA  Length:29
                                                             
                 1z9c H   1 TACAATTAAATTGTATACAATTAAATTGT  29
                                    10        20

Chain I from PDB  Type:DNA  Length:28
                                                            
                 1z9c I   2 ACAATTTAATTGTATACAATTTAATTGT  29
                                    11        21

Chain J from PDB  Type:DNA  Length:28
                                                            
                 1z9c J   1 TACAATTAAATTGTATACAATTAAATTG  28
                                    10        20

Chain K from PDB  Type:DNA  Length:29
                                                             
                 1z9c K   1 TACAATTTAATTGTATACAATTTAATTGT  29
                                    10        20

Chain L from PDB  Type:DNA  Length:28
                                                            
                 1z9c L   1 TACAATTAAATTGTATACAATTAAATTG  28
                                    10        20

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: Winged helix DNA-binding domain (576)

Family: MarR-like transcriptional regulators (34)

Protein domain: Organic hydroperoxide resistance transcriptional regulator OhrR (2)

Bacillus subtilis [TaxId: 1423] (2)

1a	d1z9ca_	A:
1b	d1z9cb_	B:
1c	d1z9cc_	C:
1d	d1z9cd_	D:
1e	d1z9ce_	E:
1f	d1z9cf_	F:

(no "CATH Domain" information available for 1Z9C)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: MarR (16)

Bacillus subtilis (3)

1a	MarR-1z9cF01	F:38-96
1b	MarR-1z9cF02	F:38-96
1c	MarR-1z9cF03	F:38-96
1d	MarR-1z9cF04	F:38-96
1e	MarR-1z9cF05	F:38-96
1f	MarR-1z9cF06	F:38-96

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (OHRR_BACSU | O34777)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic 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: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 Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1z9c)

	Sites
(no "Sites" information available for 1z9c)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1z9c)

Biological Units
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	1z9c
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	OHRR_BACSU \| O34777	:	1z91

(no "Related Entries Specified in the PDB File" available for 1Z9C)

Description

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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