1QJ8 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (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) - 10 Oct 99 (Release) - 28 Apr 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Membrane Protein, Beta-Barrel, Bacterial Defense System, Platinum Complex Structure (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	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	C8E	1	Ligand/Ion	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
2	PCL	2	Ligand/Ion	PLATINUM(II) DI-CHLORIDE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:36 , LEU A:37 , TYR A:71 , ILE A:79 , TYR A:80 , GLY A:81	BINDING SITE FOR RESIDUE C8E A 153
2	AC2	SOFTWARE	MET A:18 , MET A:21 , LYS A:48 , ASN A:60	BINDING SITE FOR RESIDUE PCL A 154
3	AC3	SOFTWARE	MET A:118	BINDING SITE FOR RESIDUE PCL A 155

(no "SS Bond" information available for 1QJ8)

Asymmetric/Biological Unit

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

(no "SAP(SNP)/Variant" information available for 1QJ8)

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 1QJ8)

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 d1qj8a_ A: Outer membrane protein X (OMPX)                                                                                                           SCOP domains
               CATH domains 1qj8A00 A:1-148  [code=2.40.160.20, no name defined]                                                                                                 CATH domains
               Pfam domains OMP_b-brl-1qj8A01 A:1-148                                                                                                                            Pfam domains
         Sec.struct. author .eeeeeeeeeeeee......eeeeeeeeeee.....eeeeeeeeeeeeeee.....eeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeee.....eeeeeeeeeeee..eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ----------------------ENT_VIR_O--------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------------------------------ENT_VIR_O PROSITE (1)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qj8 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 d1qj8a_ A: Outer membrane protein X (OMPX)                                                                                                           SCOP domains
               CATH domains 1qj8A00 A:1-148  [code=2.40.160.20, no name defined]                                                                                                 CATH domains
               Pfam domains OMP_b-brl-1qj8A01 A:1-148                                                                                                                            Pfam domains
         Sec.struct. author .eeeeeeeeeeeee......eeeeeeeeeee.....eeeeeeeeeeeeeee.....eeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeee.....eeeeeeeeeeee..eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------------------------------------------------ENT_VIR_O PROSITE (3)
                PROSITE (4) ----------------------ENT_VIR_O--------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qj8 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 d1qj8a_ A: Outer membrane protein X (OMPX)                                                                                                           SCOP domains
               CATH domains 1qj8A00 A:1-148  [code=2.40.160.20, no name defined]                                                                                                 CATH domains
               Pfam domains OMP_b-brl-1qj8A01 A:1-148                                                                                                                            Pfam domains
         Sec.struct. author .eeeeeeeeeeeee......eeeeeeeeeee.....eeeeeeeeeeeeeee.....eeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeee.....eeeeeeeeeeee..eeeeeeeeeeeee. 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
                 1qj8 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 d1qj8a_ A: Outer membrane protein X (OMPX)                                                                                                           SCOP domains
               CATH domains 1qj8A00 A:1-148  [code=2.40.160.20, no name defined]                                                                                                 CATH domains
               Pfam domains OMP_b-brl-1qj8A01 A:1-148                                                                                                                            Pfam domains
         Sec.struct. author .eeeeeeeeeeeee......eeeeeeeeeee.....eeeeeeeeeeeeeee.....eeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeee.....eeeeeeeeeeee..eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------ENT_VIR_O--------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------ENT_VIR_O PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qj8 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)

d1qj8a_

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)

1qj8A00

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-1qj8A01

A:1-148

Asymmetric/Biological Unit(hide GO term definitions)

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.

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_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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Tyr A:95 - Pro A:96	[ RasMol ]

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	1qj8
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	OMPX_ECOL6 \| P0A918
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	OMPX_ECOLI \| P0A917
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		Protein-protein Interaction	:	DIP
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	OMPX_SHIFL \| P0A920
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	OMPX_SHIFL \| P0A920
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UniProtKB/Swiss-Prot
	OMPX_ECO57 \| P0A919	:	1q9f 1qj9
	OMPX_ECOL6 \| P0A918	:	1q9f 1qj9
	OMPX_ECOLI \| P0A917	:	1orm 1q9f 1q9g 1qj9 2m06 2m07 2mnh
	OMPX_SHIFL \| P0A920	:	1q9f 1qj9

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

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SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (3, 12)

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