1QJ9 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE OUTER MEMBRANE PROTEIN OMPX FROM ESCHERICHIA COLI

Authors :   J. Vogt, G. E. Schulz

Date :   23 Jun 99 (Deposition) - 06 Oct 99 (Release) - 24 Mar 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A

Keywords :   Integral Membrane Protein, Beta Barrel, Bacterial Defense System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Vogt, G. E. Schulz
The Structure Of The Outer Membrane Protein Ompx From Escherichia Coli Reveals Mechanisms Of Virulence
Structure V. 7 1301 1999
PubMed-ID: 10545325 | Reference-DOI: 10.1016/S0969-2126(00)80063-5
(for further references see the PDB file header)

Molecule 1 - OUTER MEMBRANE PROTEIN X
	Cellular Location	:	MEMBRANE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	CYTOPLASM
	Expression System Plasmid	:	PET3B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Gene	:	OMPX
	Mutation	:	H100N
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1QJ9)

(no "Site" information available for 1QJ9)

(no "SS Bond" information available for 1QJ9)

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:95	-	Pro A:96

(no "SAP(SNP)/Variant" information available for 1QJ9)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ENT_VIR_OMP_1	PS00694	Enterobacterial virulence outer membrane protein signature 1.	OMPX_ECO57	46-54	1	A:23-31
				OMPX_ECOL6	46-54	1	A:23-31
				OMPX_ECOLI	46-54	1	A:23-31
				OMPX_SHIFL	46-54	1	A:23-31
2	ENT_VIR_OMP_2	PS00695	Enterobacterial virulence outer membrane protein signature 2.	OMPX_ECO57	163-171	1	A:140-148
				OMPX_ECOL6	163-171	1	A:140-148
				OMPX_ECOLI	163-171	1	A:140-148
				OMPX_SHIFL	163-171	1	A:140-148

(no "Exon" information available for 1QJ9)

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:148
 aligned with OMPX_ECO57 | P0A919 from UniProtKB/Swiss-Prot  Length:171

    Alignment length:148
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163        
           OMPX_ECO57    24 ATSTVTGGYAQSDAQGQMNKMGGFNLKYRYEEDNSPLGVIGSFTYTEKSRTASSGDYNKNQYYGITAGPAYRINDWASIYGVVGVGYGKFQTTEYPTYKHDTSDYGFSYGAGLQFNPMENVALDFSYEQSRIRSVDVGTWIAGVGYRF 171
               SCOP domains d1qj9a_ A: Outer membrane protein X (OMPX)                                                                                                           SCOP domains
               CATH domains 1qj9A00 A:1-148  [code=2.40.160.20, no name defined]                                                                                                 CATH domains
               Pfam domains OMP_b-brl-1qj9A01 A:1-148                                                                                                                            Pfam domains
         Sec.struct. author .eeeeeeeeeeeee.....eeeeeeeeeeee.....eeeeeeeeeeeeee......eeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeee.....eeeeeeeeee......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------ENT_VIR_O PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ----------------------ENT_VIR_O--------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qj9 A   1 ATSTVTGGYAQSDAQGQMNKMGGFNLKYRYEEDNSPLGVIGSFTYTEKSRTASSGDYNKNQYYGITAGPAYRINDWASIYGVVGVGYGKFQTTEYPTYKNDTSDYGFSYGAGLQFNPMENVALDFSYEQSRIRSVDVGTWIAGVGYRF 148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain A from PDB  Type:PROTEIN  Length:148
 aligned with OMPX_ECOL6 | P0A918 from UniProtKB/Swiss-Prot  Length:171

    Alignment length:148
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163        
           OMPX_ECOL6    24 ATSTVTGGYAQSDAQGQMNKMGGFNLKYRYEEDNSPLGVIGSFTYTEKSRTASSGDYNKNQYYGITAGPAYRINDWASIYGVVGVGYGKFQTTEYPTYKHDTSDYGFSYGAGLQFNPMENVALDFSYEQSRIRSVDVGTWIAGVGYRF 171
               SCOP domains d1qj9a_ A: Outer membrane protein X (OMPX)                                                                                                           SCOP domains
               CATH domains 1qj9A00 A:1-148  [code=2.40.160.20, no name defined]                                                                                                 CATH domains
               Pfam domains OMP_b-brl-1qj9A01 A:1-148                                                                                                                            Pfam domains
         Sec.struct. author .eeeeeeeeeeeee.....eeeeeeeeeeee.....eeeeeeeeeeeeee......eeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeee.....eeeeeeeeee......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------ENT_VIR_O--------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) -------------------------------------------------------------------------------------------------------------------------------------------ENT_VIR_O PROSITE (4)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qj9 A   1 ATSTVTGGYAQSDAQGQMNKMGGFNLKYRYEEDNSPLGVIGSFTYTEKSRTASSGDYNKNQYYGITAGPAYRINDWASIYGVVGVGYGKFQTTEYPTYKNDTSDYGFSYGAGLQFNPMENVALDFSYEQSRIRSVDVGTWIAGVGYRF 148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain A from PDB  Type:PROTEIN  Length:148
 aligned with OMPX_ECOLI | P0A917 from UniProtKB/Swiss-Prot  Length:171

    Alignment length:148
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163        
           OMPX_ECOLI    24 ATSTVTGGYAQSDAQGQMNKMGGFNLKYRYEEDNSPLGVIGSFTYTEKSRTASSGDYNKNQYYGITAGPAYRINDWASIYGVVGVGYGKFQTTEYPTYKHDTSDYGFSYGAGLQFNPMENVALDFSYEQSRIRSVDVGTWIAGVGYRF 171
               SCOP domains d1qj9a_ A: Outer membrane protein X (OMPX)                                                                                                           SCOP domains
               CATH domains 1qj9A00 A:1-148  [code=2.40.160.20, no name defined]                                                                                                 CATH domains
               Pfam domains OMP_b-brl-1qj9A01 A:1-148                                                                                                                            Pfam domains
         Sec.struct. author .eeeeeeeeeeeee.....eeeeeeeeeeee.....eeeeeeeeeeeeee......eeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeee.....eeeeeeeeee......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ----------------------ENT_VIR_O------------------------------------------------------------------------------------------------------------ENT_VIR_O PROSITE (3)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qj9 A   1 ATSTVTGGYAQSDAQGQMNKMGGFNLKYRYEEDNSPLGVIGSFTYTEKSRTASSGDYNKNQYYGITAGPAYRINDWASIYGVVGVGYGKFQTTEYPTYKNDTSDYGFSYGAGLQFNPMENVALDFSYEQSRIRSVDVGTWIAGVGYRF 148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain A from PDB  Type:PROTEIN  Length:148
 aligned with OMPX_SHIFL | P0A920 from UniProtKB/Swiss-Prot  Length:171

    Alignment length:148
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163        
           OMPX_SHIFL    24 ATSTVTGGYAQSDAQGQMNKMGGFNLKYRYEEDNSPLGVIGSFTYTEKSRTASSGDYNKNQYYGITAGPAYRINDWASIYGVVGVGYGKFQTTEYPTYKHDTSDYGFSYGAGLQFNPMENVALDFSYEQSRIRSVDVGTWIAGVGYRF 171
               SCOP domains d1qj9a_ A: Outer membrane protein X (OMPX)                                                                                                           SCOP domains
               CATH domains 1qj9A00 A:1-148  [code=2.40.160.20, no name defined]                                                                                                 CATH domains
               Pfam domains OMP_b-brl-1qj9A01 A:1-148                                                                                                                            Pfam domains
         Sec.struct. author .eeeeeeeeeeeee.....eeeeeeeeeeee.....eeeeeeeeeeeeee......eeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeee.....eeeeeeeeee......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------------ENT_VIR_O--------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------------------------------ENT_VIR_O PROSITE (1)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qj9 A   1 ATSTVTGGYAQSDAQGQMNKMGGFNLKYRYEEDNSPLGVIGSFTYTEKSRTASSGDYNKNQYYGITAGPAYRINDWASIYGVVGVGYGKFQTTEYPTYKNDTSDYGFSYGAGLQFNPMENVALDFSYEQSRIRSVDVGTWIAGVGYRF 148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Membrane and cell surface proteins and peptides (2046)

Fold: Transmembrane beta-barrels (143)

Superfamily: OMPA-like (26)

Family: Outer membrane protein (13)

Protein domain: Outer membrane protein X (OMPX) (7)

Escherichia coli [TaxId: 562] (7)

d1qj9a_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Porin (92)

Homologous Superfamily: [code=2.40.160.20, no name defined] (20)

Escherichia coli. Organism_taxid: 562. (11)

1qj9A00

A:1-148

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: MBB (97)

Family: OMP_b-brl (5)

Escherichia coli (strain K12) (4)

OMP_b-brl-1qj9A01

A:1-148

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (OMPX_ECO57 | P0A919)


GO:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain A (OMPX_ECOLI | P0A917)


GO:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain A (OMPX_ECOL6 | P0A918)


GO:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain A (OMPX_SHIFL | P0A920)


GO:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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
(no "Ligands, Modified Residues, Ions" information available for 1qj9)

	Sites
(no "Sites" information available for 1qj9)

	Cis Peptide Bonds
		Tyr A:95 - Pro A:96	[ 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 ](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
	1qj9
		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
	OMPX_ECO57 \| P0A919
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	OMPX_ECOL6 \| P0A918
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	OMPX_ECOLI \| P0A917
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	OMPX_SHIFL \| P0A920
		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
	OMPX_ECO57 \| P0A919
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	OMPX_ECOL6 \| P0A918
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	OMPX_ECOLI \| P0A917
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	OMPX_SHIFL \| P0A920
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	OMPX_ECO57 \| P0A919	:	1q9f 1qj8
	OMPX_ECOL6 \| P0A918	:	1q9f 1qj8
	OMPX_ECOLI \| P0A917	:	1orm 1q9f 1q9g 1qj8 2m06 2m07 2mnh
	OMPX_SHIFL \| P0A920	:	1q9f 1qj8

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (3, 12)

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