4W97 - JenaLib

Title :   STRUCTURE OF KETOSTEROID TRANSCRIPTIONAL REGULATOR KSTR2 OF MYCOBACTERIUM TUBERCULOSIS

Authors :   P. J. Stogios, E. Evdokimova, A. Savchenko, A. Joachimiak, Midwest Ce Structural Genomics (Mcsg)

Date :   27 Aug 14 (Deposition) - 26 Nov 14 (Release) - 21 Jan 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Cholesterol, Catabolism, Kstr2, Transcription Regulator, Tetr, Helix- Turn-Helix, Structural Genomics, Midwest Center For Structural Genomics, Mcsg, Psi-Biology, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. M. Crowe, P. J. Stogios, I. Casabon, E. Evdokimova, A. Savchenko, L. D. Eltis
Structural And Functional Characterization Of A Ketosteroid Transcriptional Regulator Of Mycobacterium Tuberculosis.
J. Biol. Chem. V. 290 872 2015
PubMed-ID: 25406313 | Reference-DOI: 10.1074/JBC.M114.607481

Compounds

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REPRESSOR KSTR2
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-41B(+)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	KSTR2, RV3557C
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	83332
	Strain	:	ATCC 25618 / H37RV

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	CL	4	Ligand/Ion	CHLORIDE ION
2	UCA	1	Ligand/Ion	S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-OXIDANYL-3-PHOSPHONOOXY-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]OXY-OXIDANYL-PHOSPHORYL]OXY-3,3-DIMETHYL-2-OXIDANYL-BUTANOYL]AMINO]PROPANOYLAMINO]ETHYL] 3-[(3AS,4S,7AS)-7A-METHYL-1,5-BIS(OXIDANYLIDENE)-2,3,3A,4,6,7-HEXAHYDROINDEN-4-YL]PROPANETHIOATE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	UCA	2	Ligand/Ion	S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-OXIDANYL-3-PHOSPHONOOXY-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]OXY-OXIDANYL-PHOSPHORYL]OXY-3,3-DIMETHYL-2-OXIDANYL-BUTANOYL]AMINO]PROPANOYLAMINO]ETHYL] 3-[(3AS,4S,7AS)-7A-METHYL-1,5-BIS(OXIDANYLIDENE)-2,3,3A,4,6,7-HEXAHYDROINDEN-4-YL]PROPANETHIOATE

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:108 , GLN A:109 , ASN A:128 , GLN A:131 , ARG A:132 , ARG A:159 , ARG A:162 , ASP A:163 , TRP A:166 , TRP A:171 , TYR A:172 , ARG A:173 , GLY A:176 , PRO A:177 , LEU A:178 , HOH A:406 , HOH A:409 , HOH A:505 , HOH A:602 , HOH A:620 , HOH A:621 , HOH A:625 , HOH A:640	binding site for residue UCA A 301
2	AC2	SOFTWARE	ASP A:153 , GLN A:186	binding site for residue CL A 302
3	AC3	SOFTWARE	ARG A:34 , THR A:179 , GLN A:181 , HOH A:473 , HOH A:551	binding site for residue CL A 303
4	AC4	SOFTWARE	ARG A:127 , GLN A:130 , HOH A:683	binding site for residue CL A 304
5	AC5	SOFTWARE	GLY A:6 , HOH A:466 , HOH A:684	binding site for residue CL A 305

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:196
                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w97 A   3 RVAGQVNSRRGELLELAAAMFAERGLRATTVRDIADGAGILSGSLYHHFASKEEMVDELLRGFLDWLFARYRDIVDSTANPLERLQGLFMASFEAIEHHHAQVVIYQDEAQRLASQPRFSYIEDRNKQQRKMWVDVLNQGIEEGYFRPDLDVDLVYRFIRDTTWVSVRWYRPGGPLTAQQVGQQYLAIVLGGITKE 198
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192

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 (6, 6)

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		UCA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4w97)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - 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
	4w97
		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
	KSTR2_MYCTU \| P9WMB9
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	KSTR2_MYCTU \| P9WMB9
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description