4Q77 - JenaLib

Title :   CRYSTAL STRUCTURE OF ROT, A GLOBAL REGULATOR OF VIRULENCE GENES IN STAPHYLOCOCCUS AUREUS

Authors :   Y. Zhu, X. Fan, X. Li, M. Teng

Date :   24 Apr 14 (Deposition) - 17 Sep 14 (Release) - 17 Sep 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.77

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

Keywords :   Winged-Helix Motif, Global Regulator, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Zhu, X. Fan, X. Zhang, X. Jiang, L. Niu, M. Teng, X. Li
Structure Of Rot, A Global Regulator Of Virulence Genes In Staphylococcus Aureus
Acta Crystallogr. , Sect. D V. 70 2467 2014
PubMed: search | Reference-DOI: 10.1107/S1399004714015326

Compounds

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REGULATOR ROT
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 34-166
	Gene	:	ROT, SAR1847
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	282458
	Strain	:	MRSA252
	Synonym	:	REPRESSOR OF TOXINS

Structural Features

Chains, Units

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:27 , GLU A:28 , SER A:31 , HOH A:216 , HOH A:218 , SER B:27 , SER B:31 , HOH B:349	BINDING SITE FOR RESIDUE GOL B 201

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:125
                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.eehhhhhhhh..hhhhhhhhhhhhhhh..eeee....eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q77 A   4 VNNDTVFGILQLETLLGDINSIFSEIESEYKMSREEILILLTLWQKGSMTLKEMDRFVEVKPYKRTRTYNNLVELEWIYKERPTVIIHFNEKLQQEKVELLNFISDAIASRATAMQNSLNAIIAV 133
                                    13        23        33        43        53        63        73        83  ||    98       108       118       128     
                                                                                                             86|                                         
                                                                                                              92

Chain B from PDB  Type:PROTEIN  Length:125
                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.eehhhhhh....hhhhhhhhhhhhhhh..eeee....eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q77 B   4 VNNDTVFGILQLETLLGDINSIFSEIESEYKMSREEILILLTLWQKGSMTLKEMDRFVEVKPYKRTRTYNNLVELEWIYKERPTVIIHFNEKLQQEKVELLNFISDAIASRATAMQNSLNAIIAV 133
                                    13        23        33        43        53        63        73        83  ||    98       108       118       128     
                                                                                                             86|                                         
                                                                                                              92

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 (5, 5)

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asn A:6 - Asp A:7	[ RasMol ]

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	4q77
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	ROT_STAAR \| Q6GFT9
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
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		Disease Information	:	OMIM

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		Age Related Information	:	GenAge

Analysis Tools

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
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Description