3C7J - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF TRANSCRIPTIONAL REGULATOR (GNTR FAMILY MEMBER) FROM PSEUDOMONAS SYRINGAE PV. TOMATO STR. DC3000

Authors :   B. Nocek, A. Sather, M. Gu, A. Joachimiak, Midwest Center For Struct Genomics (Mcsg)

Date :   07 Feb 08 (Deposition) - 26 Feb 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Transcriptional Regulator, Gntr Family, Structural Genomics, Mcsg, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Dna-Binding, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Nocek, A. Sather, M. Gu, A. Joachimiak
Structure Of Transcriptional Regulator (Gntr Family Member) From Pseudomonas Syringae Pv. Tomato Str. Dc3000.
To Be Published
PubMed: search

Molecule 1 - TRANSCRIPTIONAL REGULATOR, GNTR FAMILY
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PSPTO5454
	Organism Scientific	:	PSEUDOMONAS SYRINGAE PV. TOMATO
	Organism Taxid	:	223283
	Strain	:	DC3000

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 12)

No.	Name	Count	Type	Full Name
1	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
2	NI	2	Ligand/Ion	NICKEL (II) ION

Biological Unit 1 (1, 20)

No.	Name	Count	Type	Full Name
1	MSE	20	Mod. Amino Acid	SELENOMETHIONINE
2	NI	-1	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:144 , HIS A:148 , HIS A:192 , HIS A:214	BINDING SITE FOR RESIDUE NI A 301
2	AC2	SOFTWARE	ASN B:144 , HIS B:148 , HIS B:192 , HIS B:214	BINDING SITE FOR RESIDUE NI B 301

(no "SS Bond" information available for 3C7J)

(no "Cis Peptide Bond" information available for 3C7J)

(no "SAP(SNP)/Variant" information available for 3C7J)

(no "PROSITE Motif" information available for 3C7J)

(no "Exon" information available for 3C7J)

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:237
 aligned with Q19AK4_PSESY | Q19AK4 from UniProtKB/TrEMBL  Length:245

    Alignment length:237
                               1                                                                                                                                                                                                                                         
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       
         Q19AK4_PSESY     - ---MRKSDREAFLGSVLGNEQPPAHLARTVIEEKLRNAIIDGSLPSGTALRQQELATLFGVSRMPVREALRQLEAQSLLRVETHKGAVVAPLITEDAVDAYALRILLESEALRLSIPLLDADDLAAAKGYIEQLEVETDFGQIGRLNRMFHLSLYAKTHNKRLMRLVEEGLNEEERFLRFNLSDMGLGKLSQDDHWQLLRLAEQKAIEPCVEALQYHLNRGVQAVTQYLNSKKATKA 234
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3c7jA01 A:-2-88 'winged helix' repressor DNA binding domain                                3c7jA02 A:89-234 GntR ligand-binding domain-like                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee...eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c7j A  -2 SNAmRKSDREAFLSSVLGNEQPPAHLARTVIEEKLRNAIIDGSLPSGTALRQQELATLFGVSRmPVREALRQLEAQSLLRVETHKGAVVAPLITEDAVDAYALRILLESEALRLSIPLLDADDLAAAASYIEQLEVETDFGQIGRLNRmFHLSLYAKTHNKRLmRLVEEGLNEEERFLRFNLSSmGLGKLSQDDHWQLLRLAEQKAVEPCVEALQYHLNRGVQAVTQYLQSQKAGNV 234
                               |     7        17        27        37        47        57   |    67        77        87        97       107       117       127       137       147       157   |   167       177    |  187       197       207       217       227       
                               |                                                          61-MSE                                                                              146-MSE        161-MSE              182-MSE                                                
                               1-MSE

Chain A from PDB  Type:PROTEIN  Length:237
 aligned with Q87U60_PSESM | Q87U60 from UniProtKB/TrEMBL  Length:245

    Alignment length:237
                               1                                                                                                                                                                                                                                         
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       
         Q87U60_PSESM     - ---MRKSDREAFLSSVLGNEQPPAHLARTVIEEKLRNAIIDGSLPSGTALRQQELATLFGVSRMPVREALRQLEAQSLLRVETHKGAVVAPLITEDAVDAYALRILLESEALRLSIPLLDADDLAAAASYIEQLEVETDFGQIGRLNRMFHLSLYAKTHNKRLMRLVEEGLNEEERFLRFNLSSMGLGKLSQDDHWQLLRLAEQKAVEPCVEALQYHLNRGVQAVTQYLQSQKAGNV 234
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3c7jA01 A:-2-88 'winged helix' repressor DNA binding domain                                3c7jA02 A:89-234 GntR ligand-binding domain-like                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee...eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c7j A  -2 SNAmRKSDREAFLSSVLGNEQPPAHLARTVIEEKLRNAIIDGSLPSGTALRQQELATLFGVSRmPVREALRQLEAQSLLRVETHKGAVVAPLITEDAVDAYALRILLESEALRLSIPLLDADDLAAAASYIEQLEVETDFGQIGRLNRmFHLSLYAKTHNKRLmRLVEEGLNEEERFLRFNLSSmGLGKLSQDDHWQLLRLAEQKAVEPCVEALQYHLNRGVQAVTQYLQSQKAGNV 234
                               |     7        17        27        37        47        57   |    67        77        87        97       107       117       127       137       147       157   |   167       177    |  187       197       207       217       227       
                               1-MSE                                                      61-MSE                                                                              146-MSE        161-MSE              182-MSE

Chain B from PDB  Type:PROTEIN  Length:227
 aligned with Q19AK4_PSESY | Q19AK4 from UniProtKB/TrEMBL  Length:245

    Alignment length:232
                               1                                                                                                                                                                                                                                    
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227  
         Q19AK4_PSESY     - ---MRKSDREAFLGSVLGNEQPPAHLARTVIEEKLRNAIIDGSLPSGTALRQQELATLFGVSRMPVREALRQLEAQSLLRVETHKGAVVAPLITEDAVDAYALRILLESEALRLSIPLLDADDLAAAKGYIEQLEVETDFGQIGRLNRMFHLSLYAKTHNKRLMRLVEEGLNEEERFLRFNLSDMGLGKLSQDDHWQLLRLAEQKAIEPCVEALQYHLNRGVQAVTQYLNSK 229
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3c7jB01 B:-2-88 'winged helix' repressor DNA binding domain                                3c7jB02 B:89-229 GntR ligand-binding domain-like                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee...eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...-----.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c7j B  -2 SNAmRKSDREAFLSSVLGNEQPPAHLARTVIEEKLRNAIIDGSLPSGTALRQQELATLFGVSRmPVREALRQLEAQSLLRVETHKGAVVAPLITEDAVDAYALRILLESEALRLSIPLLDADDLAAAASYIEQLEVETDFGQIGRLNRmFHLSLYAKTHNKRLmRLVEEGLNEEERFLRFNLSSm-----SQDDHWQLLRLAEQKAVEPCVEALQYHLNRGVQAVTQYLQSQ 229
                               |     7        17        27        37        47        57   |    67        77        87        97       107       117       127       137       147       157   |   167       177    |    -|      197       207       217       227  
                               1-MSE                                                      61-MSE                                                                              146-MSE        161-MSE              182-MSE88

Chain B from PDB  Type:PROTEIN  Length:227
 aligned with Q87U60_PSESM | Q87U60 from UniProtKB/TrEMBL  Length:245

    Alignment length:232
                               1                                                                                                                                                                                                                                    
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227  
         Q87U60_PSESM     - ---MRKSDREAFLSSVLGNEQPPAHLARTVIEEKLRNAIIDGSLPSGTALRQQELATLFGVSRMPVREALRQLEAQSLLRVETHKGAVVAPLITEDAVDAYALRILLESEALRLSIPLLDADDLAAAASYIEQLEVETDFGQIGRLNRMFHLSLYAKTHNKRLMRLVEEGLNEEERFLRFNLSSMGLGKLSQDDHWQLLRLAEQKAVEPCVEALQYHLNRGVQAVTQYLQSQ 229
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3c7jB01 B:-2-88 'winged helix' repressor DNA binding domain                                3c7jB02 B:89-229 GntR ligand-binding domain-like                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee...eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...-----.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c7j B  -2 SNAmRKSDREAFLSSVLGNEQPPAHLARTVIEEKLRNAIIDGSLPSGTALRQQELATLFGVSRmPVREALRQLEAQSLLRVETHKGAVVAPLITEDAVDAYALRILLESEALRLSIPLLDADDLAAAASYIEQLEVETDFGQIGRLNRmFHLSLYAKTHNKRLmRLVEEGLNEEERFLRFNLSSm-----SQDDHWQLLRLAEQKAVEPCVEALQYHLNRGVQAVTQYLQSQ 229
                               |     7        17        27        37        47        57   |    67        77        87        97       107       117       127       137       147       157   |   167       177    |    -|      197       207       217       227  
                               1-MSE                                                      61-MSE                                                                              146-MSE        161-MSE              182-MSE88

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 3C7J)

(no "Pfam Domain" information available for 3C7J)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q87U60_PSESM | Q87U60)

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.

Chain A,B (Q19AK4_PSESY | Q19AK4)

molecular function
	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.

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
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NI	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3c7j)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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)

Access by PDB/NDB ID
	3c7j
		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
	Q19AK4_PSESY \| Q19AK4
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL
	Q87U60_PSESM \| Q87U60
		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

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
	Q19AK4_PSESY \| Q19AK4
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	Q87U60_PSESM \| Q87U60
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 3C7J)

(no "Related Entries Specified in the PDB File" available for 3C7J)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 12)

Sites (2, 2)

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

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (2, 4)

Pfam Domains (0, 0)

Gene Ontology (4, 6)

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