1DCM - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF UNPHOSPHORYLATED FIXJ-N WITH AN ATYPICAL CONFORMER (MONOMER A)

Authors :   P. Gouet, B. Fabry, V. Guillet, C. Birck, L. Mourey, D. Kahn, J. P. Samama

Date :   05 Nov 99 (Deposition) - 08 Nov 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Doubly Wound Five-Stranded Beta/Alpha Fold, Nitrogen Fixation Regulation, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Gouet, B. Fabry, V. Guillet, C. Birck, L. Mourey, D. Kahn, J. P. Samama
Structural Transitions In The Fixj Receiver Domain.
Structure Fold. Des. V. 7 1517 1999
PubMed-ID: 10647182 | Reference-DOI: 10.1016/S0969-2126(00)88342-2
(for further references see the PDB file header)

Molecule 1 - TRANSCRIPTIONAL REGULATORY PROTEIN FIXJ
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PT7-7
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	FIXJ RECEIVER DOMAIN (RESIDUES 1-126)
	Mutation	:	YES
	Organism Scientific	:	SINORHIZOBIUM MELILOTI
	Organism Taxid	:	382

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:11 , ASP B:54 , ARG B:56	BINDING SITE FOR RESIDUE MG B 127

(no "SS Bond" information available for 1DCM)

Asymmetric Unit

No.	Residues
1	Lys A:104	-	Pro A:105
2	Lys B:104	-	Pro B:105

(no "SAP(SNP)/Variant" information available for 1DCM)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RESPONSE_REGULATORY	PS50110	Response regulatory domain profile.	FIXJ_RHIME	5-119	2	A:5-119 B:5-119

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RESPONSE_REGULATORY	PS50110	Response regulatory domain profile.	FIXJ_RHIME	5-119	1	A:5-119 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RESPONSE_REGULATORY	PS50110	Response regulatory domain profile.	FIXJ_RHIME	5-119	1	- B:5-119

(no "Exon" information available for 1DCM)

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:121
 aligned with FIXJ_RHIME | P10958 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:121
                                    12        22        32        42        52        62        72        82        92       102       112       122 
           FIXJ_RHIME     3 DYTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAPDVRNGVLVTDLRMPDMSGVELLRNLGDLKINIPSIVITGHGDVPMAVEAMKAGAVDFIEKPFEDTVIIEAIERASEHLV 123
               SCOP domains d1dcma_ A: Transcriptional regulatory protein FixJ, receiver domain                                                       SCOP domains
               CATH domains 1dcmA00 A:3-123  [code=3.40.50.2300, no name defined]                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..........hhhhhhhh..eee...hhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh.......eeee...hhhhhhhhhh....eeee...hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RESPONSE_REGULATORY  PDB: A:5-119 UniProt: 5-119                                                                   ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dcm A   3 DYTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAPDVRNGVLVTDLRMPDMSGVELLRNLGDLKINIPSIVITGHGDVPMAVEAMKAGAVDFIEKPFEDTVIIEAIERASEHLV 123
                                    12        22        32        42        52        62        72        82        92       102       112       122

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with FIXJ_RHIME | P10958 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:121
                                    12        22        32        42        52        62        72        82        92       102       112       122 
           FIXJ_RHIME     3 DYTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAPDVRNGVLVTDLRMPDMSGVELLRNLGDLKINIPSIVITGHGDVPMAVEAMKAGAVDFIEKPFEDTVIIEAIERASEHLV 123
               SCOP domains d1dcmb_ B: Transcriptional regulatory protein FixJ, receiver domain                                                       SCOP domains
               CATH domains 1dcmB00 B:3-123  [code=3.40.50.2300, no name defined]                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhh..eeeeee......hhhhhhhhhhhh.....eeee....hhhhhhhhhh....eee....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RESPONSE_REGULATORY  PDB: B:5-119 UniProt: 5-119                                                                   ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dcm B   3 DYTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAPDVRNGVLVTDLRMPDMSGVELLRNLGDLKINIPSIVITGHGDVPMAVEAMKAGAVDFIEKPFEDTVIIEAIERASEHLV 123
                                    12        22        32        42        52        62        72        82        92       102       112       122

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Flavodoxin-like (1057)

Superfamily: CheY-like (258)

Family: CheY-related (166)

Protein domain: Transcriptional regulatory protein FixJ, receiver domain (4)

Rhizobium meliloti [TaxId: 382] (4)

1a	d1dcma_	A:
1b	d1dcmb_	B:

Asymmetric 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)

Sinorhizobium meliloti. Organism_taxid: 382. (6)

1a	1dcmA00	A:3-123
1b	1dcmB00	B:3-123

(no "Pfam Domain" information available for 1DCM)

Asymmetric Unit(hide GO term definitions)

Chain A,B (FIXJ_RHIME | P10958)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0009399	nitrogen fixation	The process in which nitrogen is taken from its relatively inert molecular form (N2) in the atmosphere and converted into nitrogen compounds useful for other chemical processes, such as ammonia, nitrate and nitrogen dioxide.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Lys A:104 - Pro A:105	[ RasMol ]
		Lys B:104 - Pro B:105	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ 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 \| Biol. Unit 2 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
	1dcm
		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
	FIXJ_RHIME \| P10958
		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
	FIXJ_RHIME \| P10958
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	FIXJ_RHIME \| P10958	:	1d5w 1dbw 1dck 1x3u

1d5w	STRUCTURE OF PHOSPHORYLATED FIXJN
1dbw	STRUCTURE OF UNPHOSPHORYLATED FIXJN
1dck	STRUCTURE OF UNPHOSPHORYLATED FIXJN COMPLEXED WITH MN2+

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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