3DZD - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF SIGMA54 ACTIVATOR NTRC4 IN THE INACTIVE STATE

Authors :   J. D. Batchelor, M. Doucleff, C. -J. Lee, K. Matsubara, S. De Carlo, J. Heideker, M. M. Lamers, J. G. Pelton, D. E. Wemmer

Date :   29 Jul 08 (Deposition) - 25 Nov 08 (Release) - 09 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Sigma43 Activator, Aaa+ Atpase, Response Regulator, Transcriptional Activator, Atp-Binding, Nucleotide-Binding, Transcription, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. D. Batchelor, M. Doucleff, C. J. Lee, K. Matsubara, S. De Carlo, J. Heideker, M. H. Lamers, J. G. Pelton, D. E. Wemmer
Structure And Regulatory Mechanism Of Aquifex Aeolicus Ntrc4: Variability And Evolution In Bacterial Transcriptional Regulation.
J. Mol. Biol. V. 384 1058 2008
PubMed-ID: 18955063 | Reference-DOI: 10.1016/J.JMB.2008.10.024
(for further references see the PDB file header)

Molecule 1 - TRANSCRIPTIONAL REGULATOR (NTRC FAMILY)
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSKB3
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 2 TO 369
	Gene	:	AQ_164, NTRC4
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 7)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
3	NA	1	Ligand/Ion	SODIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:131 , PHE A:132 , VAL A:133 , GLY A:163 , THR A:164 , GLY A:165 , LYS A:166 , GLU A:167 , ILE A:168 , LEU A:312 , VAL A:348 , LYS A:352 , HOH A:412 , HOH A:442 , HOH A:484 , HOH A:487	BINDING SITE FOR RESIDUE ADP A 370
2	AC2	SOFTWARE	GLU B:131 , PHE B:132 , VAL B:133 , GLY B:163 , THR B:164 , GLY B:165 , LYS B:166 , GLU B:167 , ILE B:168 , LEU B:312 , VAL B:348 , ARG B:349 , HOH B:406	BINDING SITE FOR RESIDUE ADP B 370
3	AC3	SOFTWARE	GLU B:231 , GLY B:233 , THR B:271 , LYS B:273	BINDING SITE FOR RESIDUE NA B 1

Asymmetric/Biological Unit

No.	Residues
1	A:328	-	A:362
2	B:328	-	B:362

Asymmetric/Biological Unit

No.	Residues
1	Lys A:102	-	Pro A:103
2	Lys B:102	-	Pro B:103

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

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

(no "Exon" information available for 3DZD)

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:368
 aligned with O66551_AQUAE | O66551 from UniProtKB/TrEMBL  Length:442

    Alignment length:368
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361        
         O66551_AQUAE     2 KRVLVVDDEESITSSLSAILEEEGYHPDTAKTLREAEKKIKELFFPVIVLDVWMPDGDGVNFIDFIKENSPDSVVIVITGHGSVDTAVKAIKKGAYEFLEKPFSVERFLLTIKHAFEEYSKKAPPQEEIEFVGEHPKILEIKRLIPKIAKSKAPVLITGESGTGKEIVARLIHRYSGRKGAFVDLNCASIPQELAESELFGHEKGAFTGALTRKKGKLELADQGTLFLDEVGELDQRVQAKLLRVLETGSFTRLGGNQKIEVDIRVISATNKNLEEEIKKGNFREDLYYRLSVFQIYLPPLRERGKDVILLAEYFLKKFAKEYKKNCFELSEETKEYLMKQEWKGNVRELKNLIERAVILCEGEVIKP 369
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3dzdA01 A:2-122  [code=3.40.50.2300, no name defined]                                                                    -------------3dzdA02 A:136-300 P-loop containing nucleotide triphosphate hydrolases                                                                                               3dzdA03 A:301-369  [code=1.10.8.60, no name defined]                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh...eeeee.ee..ee..hhhhhhhhhh...eeeeee....hhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhh....eeeee.......hhhhhhhee...........eehhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhee........ee...eeeeee..hhhhhhhh...hhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh....hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dzd A   2 KRVLVVDDEESITSSLSAILEEEGYHPDTAKTLREAEKKIKELFFPVIVLDVWmPDGDGVNFIDFIKENSPDSVVIVITGHGSVDTAVKAIKKGAYEFLEKPFSVERFLLTIKHAFEEYSKKAPPQEEIEFVGEHPKILEIKRLIPKIAKSKAPVLITGESGTGKEIVARLIHRYSGRKGAFVDLNCASIPQELAESELFGHEKGAFTGALTRKKGKLELADQGTLFLDEVGELDQRVQAKLLRVLETGSFTRLGGNQKIEVDIRVISATNKNLEEEIKKGNFREDLYYRLSVFQIYLPPLRERGKDVILLAEYFLKKFAKEYKKNCFELSEETKEYLmKQEWKGNVRELKNLIERAVILCEGEVIKP 369
                                    11        21        31        41        51   |    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361        
                                                                                55-MSE                                                                                                                                                                                                                                                                                      340-MSE

Chain B from PDB  Type:PROTEIN  Length:368
 aligned with O66551_AQUAE | O66551 from UniProtKB/TrEMBL  Length:442

    Alignment length:368
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361        
         O66551_AQUAE     2 KRVLVVDDEESITSSLSAILEEEGYHPDTAKTLREAEKKIKELFFPVIVLDVWMPDGDGVNFIDFIKENSPDSVVIVITGHGSVDTAVKAIKKGAYEFLEKPFSVERFLLTIKHAFEEYSKKAPPQEEIEFVGEHPKILEIKRLIPKIAKSKAPVLITGESGTGKEIVARLIHRYSGRKGAFVDLNCASIPQELAESELFGHEKGAFTGALTRKKGKLELADQGTLFLDEVGELDQRVQAKLLRVLETGSFTRLGGNQKIEVDIRVISATNKNLEEEIKKGNFREDLYYRLSVFQIYLPPLRERGKDVILLAEYFLKKFAKEYKKNCFELSEETKEYLMKQEWKGNVRELKNLIERAVILCEGEVIKP 369
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3dzdB01 B:2-122  [code=3.40.50.2300, no name defined]                                                                    -------------3dzdB02 B:136-300 P-loop containing nucleotide triphosphate hydrolases                                                                                               3dzdB03 B:301-369  [code=1.10.8.60, no name defined]                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh...eeeee.ee..ee..hhhhhhhhhh...eeeeee....hhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhh....eeeee......hhhhhhhhee...........eehhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhee........ee...eeeeee..hhhhhhhh...hhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhh.....hhhhhhhhhhhhhhhh....ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dzd B   2 KRVLVVDDEESITSSLSAILEEEGYHPDTAKTLREAEKKIKELFFPVIVLDVWmPDGDGVNFIDFIKENSPDSVVIVITGHGSVDTAVKAIKKGAYEFLEKPFSVERFLLTIKHAFEEYSKKAPPQEEIEFVGEHPKILEIKRLIPKIAKSKAPVLITGESGTGKEIVARLIHRYSGRKGAFVDLNCASIPQELAESELFGHEKGAFTGALTRKKGKLELADQGTLFLDEVGELDQRVQAKLLRVLETGSFTRLGGNQKIEVDIRVISATNKNLEEEIKKGNFREDLYYRLSVFQIYLPPLRERGKDVILLAEYFLKKFAKEYKKNCFELSEETKEYLmKQEWKGNVRELKNLIERAVILCEGEVIKP 369
                                    11        21        31        41        51   |    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361        
                                                                                55-MSE                                                                                                                                                                                                                                                                                      340-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 3DZD)

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (O66551_AQUAE | O66551)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
	GO:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
	GO:0000160	phosphorelay signal transduction system	A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
	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.
cellular component
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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
		ADP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
		Lys A:102 - Pro A:103	[ RasMol ]
		Lys B:102 - Pro B:103	[ 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
	3dzd
		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
	O66551_AQUAE \| O66551
		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
	O66551_AQUAE \| O66551
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	O66551_AQUAE \| O66551	:	1zit 2jrl 3e7l 4fth

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (3, 3)

SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

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 (3, 6)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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