3CLK - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A TRANSCRIPTION REGULATOR FROM LACTOBACILLUS PLANTARUM

Authors :   R. Sugadev, S. K. Burley, S. Swaminathan, New York Sgx Research Cen Structural Genomics (Nysgxrc)

Date :   19 Mar 08 (Deposition) - 01 Apr 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.08

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

Keywords :   11017J, Psi-Ii, Nysgxrc, Dimer, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Dna-Binding, Transcription, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Sugadev, S. K. Burley, S. Swaminathan
Crystal Structure Of A Transcription Regulator From Lactobacillus Plantarum.
To Be Published
PubMed: search

Molecule 1 - TRANSCRIPTION REGULATOR
	Atcc	:	BAA-793
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PSGX3(BC)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 57-335
	Organism Scientific	:	LACTOBACILLUS PLANTARUM WCFS1
	Organism Taxid	:	220668
	Strain	:	WCFS1 / NCIMB 8826

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 13)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:73 , PHE A:75 , ARG A:196 , TYR A:221 , ALA A:245 , ASP A:274 , GLN A:291	BINDING SITE FOR RESIDUE GOL A 500

(no "SS Bond" information available for 3CLK)

Asymmetric/Biological Unit

No.	Residues
1	Val A:264	-	Pro A:265
2	Arg A:283	-	Pro A:284
3	Val B:264	-	Pro B:265
4	Arg B:283	-	Pro B:284

(no "SAP(SNP)/Variant" information available for 3CLK)

(no "PROSITE Motif" information available for 3CLK)

(no "Exon" information available for 3CLK)

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:251
 aligned with F9ULH5_LACPL | F9ULH5 from UniProtKB/TrEMBL  Length:335

    Alignment length:274
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330    
         F9ULH5_LACPL    61 SNVIAAVVSSVRTNFAQQILDGIQEEAHKNGYNLIIVYSGSADPEEQKHALLTAIERPVMGILLLSIALTDDNLQLLQSSDVPYCFLSMGFDDDRPFISSDDEDIGYQATNLLINEGHRQIGIAGIDQYPYTGRKRLAGYKKALKEANIAINQEWIKPGDYSYTSGEQAMKAFGKNTDLTGIIAASDMTAIGILNQASSFGIEVPKDLSIVSIDGTEMCKITRPQLTSISQDFFQMGVTGVQQIHQSVKNGSNRIVSQQFIPVNPVIRKSTARL 334
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3clkA01 A:61-161,A:291-323  [code=3.40          .50.2300, no name de    fined]                       3clkA02 A:162-290,A:324-334  [code=3.40.50.2300, no name defined]                                                                3clkA01 A:61-161,A:     291-323  3clkA02     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......hhhhhhhhhhhhhhhh...eeeee.----------hhhhhhhh....eeeee...----hhhhhhh.--.eeee...--....eee.hhhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhhhhhh....hhh.ee....hhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhh........eeeeee..hhhhhh....eeee.hhhhhhhhhhhhhhhhh.-----...eee...eee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3clk A  61 SNVIAAVVSSVRTNFAQQILDGIQEEAHKNGYNLIIVY----------HALLTAIERPVmGILLLSIA----NLQLLQSS--PYCFLSmG--DDRPFISSDDEDIGYQATNLLINEGHRQIGIAGIDQYPYTGRKRLAGYKKALKEANIAINQEWIKPGDYSYTSGEQAmKAFGKNTDLTGIIAASDmTAIGILNQASSFGIEVPKDLSIVSIDGTEmCKITRPQLTSISQDFFQmGVTGVQQIHQSVK-----IVSQQFIPVNPVIRKSTARL 334
                                    70        80        90       | -       110       120       | -  |    140  |    150  |    160       170       180       190       200       210       220       230       240       250       260       270       280       290     | 300        |-    |  320       330    
                                                                98        109        120-MSE 128  133    140  |     ||  |                                                                          230-MSE           248-MSE                       278-MSE           296-MSE      309   315                   
                                                                                                            143     ||  |                                                                                                                                                                                     
                                                                                                                  149-MSE                                                                                                                                                                                     
                                                                                                                   150  |                                                                                                                                                                                     
                                                                                                                      153

Chain B from PDB  Type:PROTEIN  Length:262
 aligned with F9ULH5_LACPL | F9ULH5 from UniProtKB/TrEMBL  Length:335

    Alignment length:272
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332  
         F9ULH5_LACPL    63 VIAAVVSSVRTNFAQQILDGIQEEAHKNGYNLIIVYSGSADPEEQKHALLTAIERPVMGILLLSIALTDDNLQLLQSSDVPYCFLSMGFDDDRPFISSDDEDIGYQATNLLINEGHRQIGIAGIDQYPYTGRKRLAGYKKALKEANIAINQEWIKPGDYSYTSGEQAMKAFGKNTDLTGIIAASDMTAIGILNQASSFGIEVPKDLSIVSIDGTEMCKITRPQLTSISQDFFQMGVTGVQQIHQSVKNGSNRIVSQQFIPVNPVIRKSTARL 334
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3clkB01     B:63-161,B:291-323  [cod      e=3.40.50.2300, no name defined]                         3clkB02 B:162-290,B:324-334  [code=3.40.50.2300, no name defined]                                                                3clkB01 B:63-161,B:291-323       3clkB02     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.----hhhhhhhhhhhhhhh.....eeee.------hhhhhhhhhhhhh...eeeee....hhhhhhhhhhh...eeee.........eee.hhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhhhhh....hhh.ee....hhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhh........eeeeee.hhhhhh.....eeee.hhhhhhhhhhhhhhhhhhh.......eee...eee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3clk B  63 VIAAVVS----NFAQQILDGIQEEAHKNGYNLIIVY------EEQKHALLTAIERPVmGILLLSIALTDDNLQLLQSSDVPYCFLSmGFDDDRPFISSDDEDIGYQATNLLINEGHRQIGIAGIDQYPYTGRKRLAGYKKALKEANIAINQEWIKPGDYSYTSGEQAmKAFGKNTDLTGIIAASDmTAIGILNQASSFGIEVPKDLSIVSIDGTEmCKITRPQLTSISQDFFQmGVTGVQQIHQSVKNGSNRIVSQQFIPVNPVIRKSTARL 334
                                  |  - |      82        92     |   -  |    112       122       132       142      |152       162       172       182       192       202       212       222       232       242     | 252       262       272     | 282       292   |   302       312       322       332  
                                 69   74                      98    105            120-MSE                      149-MSE                                                                          230-MSE           248-MSE                       278-MSE           296-MSE

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 '\|'

(no "SCOP Domain" information available for 3CLK)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.2300, no name defined] (308)

Lactobacillus plantarum wcfs1. Organism_taxid: 220668. Strain: wcfs1 /ncimb 8826. (1)

1a	3clkA02	A:162-290,A:324-334
1b	3clkB02	B:162-290,B:324-334
1c	3clkB01	B:63-161,B:291-323
1d	3clkA01	A:61-161,A:291-323

(no "Pfam Domain" information available for 3CLK)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (F9ULH5_LACPL | F9ULH5)

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.
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.

Asymmetric/Biological 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
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Arg A:283 - Pro A:284	[ RasMol ]
		Arg B:283 - Pro B:284	[ RasMol ]
		Val A:264 - Pro A:265	[ RasMol ]
		Val B:264 - Pro B:265	[ RasMol ]

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)

Access by PDB/NDB ID
	3clk
		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
	F9ULH5_LACPL \| F9ULH5
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

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

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
	F9ULH5_LACPL \| F9ULH5
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 3CLK)

(no "Related Entries Specified in the PDB File" available for 3CLK)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 13)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (4, 4)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File