3VW1 - JenaLib

Title :   CRYSTAL STRUCUTURE OF THE CRYSTAL VIOLET-BOUND FORM OF RAMR (TRANSCRIPTIONAL REGURATOR OF TETR FAMILY) FROM SALMONELLA TYPHIMURIUM

Authors :   K. Sakurai, S. Yamasaki, R. Nakashima, E. Nikaido, A. Yamaguchi, K. Nis

Date :   30 Jul 12 (Deposition) - 03 Jul 13 (Release) - 24 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.21

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

Keywords :   Tetr Transcriptional Regulator Family, Hth-Motif, Transcriptional Regulator, Dna Binding, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Yamasaki, E. Nikaido, R. Nakashima, K. Sakurai, D. Fujiwara, I. Fujii, K. Nishino
The Crystal Structure Of Multidrug-Resistance Regulator Ram With Multiple Drugs
Nat Commun V. 4 2078 2013
PubMed-ID: 23800819 | Reference-DOI: 10.1038/NCOMMS3078

Compounds

Molecule 1 - PUTATIVE REGULATORY PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET DUET
	Expression System Strain	:	C41(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	STM0580, STM14_0676
	Organism Scientific	:	SALMONELLA TYPHIMURIUM
	Organism Taxid	:	588858
	Strain	:	14028S
	Synonym	:	RAMR, TETR-LIKE TRANSCRIPTIONAL REGULATOR

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 7)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	CVI	2	Ligand/Ion	CRYSTAL VIOLET
3	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	CVI	1	Ligand/Ion	CRYSTAL VIOLET
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	CVI	1	Ligand/Ion	CRYSTAL VIOLET
3	SO4	2	Ligand/Ion	SULFATE ION

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:19 , HIS A:99 , PRO A:100 , ALA A:101 , ARG A:102	BINDING SITE FOR RESIDUE SO4 A 201
2	AC2	SOFTWARE	ARG A:35 , LYS D:51	BINDING SITE FOR RESIDUE CL A 202
3	AC3	SOFTWARE	TYR B:59 , LEU B:66 , CYS B:67 , MET B:70 , ILE B:88 , SER B:91 , TYR B:92 , ILE B:106 , LEU B:130 , PHE B:155 , HOH B:410	BINDING SITE FOR RESIDUE CVI B 301
4	AC4	SOFTWARE	GLN B:19 , HIS B:99 , PRO B:100 , ALA B:101 , ARG B:102	BINDING SITE FOR RESIDUE SO4 B 302
5	AC5	SOFTWARE	GLN C:19 , HIS C:99 , PRO C:100 , ALA C:101 , ARG C:102	BINDING SITE FOR RESIDUE SO4 C 201
6	AC6	SOFTWARE	TYR D:59 , CYS D:67 , MET D:70 , ILE D:88 , SER D:91 , ILE D:106 , PHE D:127 , LEU D:130 , CYS D:134 , VAL D:138 , PHE D:155	BINDING SITE FOR RESIDUE CVI D 301
7	AC7	SOFTWARE	GLN D:19 , ASN D:98 , HIS D:99 , PRO D:100 , ALA D:101 , ARG D:102 , HOH D:414	BINDING SITE FOR RESIDUE SO4 D 302

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:184
 aligned with A0A0F6AY66_S | A0A0F6AY66 from UniProtKB/TrEMBL  Length:193

    Alignment length:184
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187    
         A0A0F6AY66_S     8 DKKQALLEAATQAIAQSGIAASTAVIARNAGVAEGTLFRYFATKDELINTLYLHLKQDLCQSMIMELDRSITDAKMMTRFIWNSYISWGLNHPARHRAIRQLAVSEKLTKETEQRADDMFPELRDLCHRSVLMVFMSDEYRAFGDGLFLALAETTMDFAARDPARAGEYIALGFEAMWRALTRE 191
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vw1 A   8 DKKQALLEAATQAIAQSGIAASTAVIARNAGVAEGTLFRYFATKDELINTLYLHLKQDLCQSMIMELDRSITDAKMMTRFIWNSYISWGLNHPARHRAIRQLAVSEKLTKETEQRADDMFPELRDLCHRSVLMVFMSDEYRAFGDGLFLALAETTMDFAARDPARAGEYIALGFEAMWRALTRE 191
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187

Chain B from PDB  Type:PROTEIN  Length:184
 aligned with A0A0F6AY66_S | A0A0F6AY66 from UniProtKB/TrEMBL  Length:193

    Alignment length:184
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187    
         A0A0F6AY66_S     8 DKKQALLEAATQAIAQSGIAASTAVIARNAGVAEGTLFRYFATKDELINTLYLHLKQDLCQSMIMELDRSITDAKMMTRFIWNSYISWGLNHPARHRAIRQLAVSEKLTKETEQRADDMFPELRDLCHRSVLMVFMSDEYRAFGDGLFLALAETTMDFAARDPARAGEYIALGFEAMWRALTRE 191
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...hhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vw1 B   8 DKKQALLEAATQAIAQSGIAASTAVIARNAGVAEGTLFRYFATKDELINTLYLHLKQDLCQSMIMELDRSITDAKMMTRFIWNSYISWGLNHPARHRAIRQLAVSEKLTKETEQRADDMFPELRDLCHRSVLMVFMSDEYRAFGDGLFLALAETTMDFAARDPARAGEYIALGFEAMWRALTRE 191
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187

Chain C from PDB  Type:PROTEIN  Length:184
 aligned with A0A0F6AY66_S | A0A0F6AY66 from UniProtKB/TrEMBL  Length:193

    Alignment length:184
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187    
         A0A0F6AY66_S     8 DKKQALLEAATQAIAQSGIAASTAVIARNAGVAEGTLFRYFATKDELINTLYLHLKQDLCQSMIMELDRSITDAKMMTRFIWNSYISWGLNHPARHRAIRQLAVSEKLTKETEQRADDMFPELRDLCHRSVLMVFMSDEYRAFGDGLFLALAETTMDFAARDPARAGEYIALGFEAMWRALTRE 191
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vw1 C   8 DKKQALLEAATQAIAQSGIAASTAVIARNAGVAEGTLFRYFATKDELINTLYLHLKQDLCQSMIMELDRSITDAKMMTRFIWNSYISWGLNHPARHRAIRQLAVSEKLTKETEQRADDMFPELRDLCHRSVLMVFMSDEYRAFGDGLFLALAETTMDFAARDPARAGEYIALGFEAMWRALTRE 191
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187

Chain D from PDB  Type:PROTEIN  Length:183
 aligned with A0A0F6AY66_S | A0A0F6AY66 from UniProtKB/TrEMBL  Length:193

    Alignment length:183
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187   
         A0A0F6AY66_S     8 DKKQALLEAATQAIAQSGIAASTAVIARNAGVAEGTLFRYFATKDELINTLYLHLKQDLCQSMIMELDRSITDAKMMTRFIWNSYISWGLNHPARHRAIRQLAVSEKLTKETEQRADDMFPELRDLCHRSVLMVFMSDEYRAFGDGLFLALAETTMDFAARDPARAGEYIALGFEAMWRALTR 190
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vw1 D   8 DKKQALLEAATQAIAQSGIAASTAVIARNAGVAEGTLFRYFATKDELINTLYLHLKQDLCQSMIMELDRSITDAKMMTRFIWNSYISWGLNHPARHRAIRQLAVSEKLTKETEQRADDMFPELRDLCHRSVLMVFMSDEYRAFGDGLFLALAETTMDFAARDPARAGEYIALGFEAMWRALTR 190
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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