3HW9 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CATION SELECTIVE PATHWAY OF OMPF PORIN REVEALED BY ANOMALOUS X-RAY DIFFRACTION

Authors :   D. Balasundaresan, S. Raychaudhury, L. Blachowicz, B. Roux

Date :   17 Jun 09 (Deposition) - 08 Dec 09 (Release) - 09 Mar 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.61

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (3x)
Biol. Unit 2: B  (3x)
Biol. Unit 3: A,B  (1x)

Keywords :   Porin, Membrane Protein, Integral Membrane Protein Porin, Cell Membrane, Cell Outer Membrane, Ion Transport, Membrane, Phage Recognition, Transmembrane, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Dhakshnamoorthy, S. Raychaudhury, L. Blachowicz, B. Roux
Cation-Selective Pathway Of Ompf Porin Revealed By Anomalous X-Ray Diffraction.
J. Mol. Biol. V. 396 293 2010
PubMed-ID: 19932117 | Reference-DOI: 10.1016/J.JMB.2009.11.042

Molecule 1 - OUTER MEMBRANE PROTEIN F
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PPR272
	Expression System Strain	:	MH225
	Expression System Taxid	:	562
	Gene	:	B0929, CMLB, COA, CRY, JW0912, OMPF, TOLF
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K-12
	Synonym	:	PORIN OMPF, OUTER MEMBRANE PROTEIN 1A, OUTER MEMBRANE PROTEIN IA, OUTER MEMBRANE PROTEIN B

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (3x)	:	A
Biological Unit 2 (3x)	:		B
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	K	4	Ligand/Ion	POTASSIUM ION
3	P6G	2	Ligand/Ion	HEXAETHYLENE GLYCOL

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	K	-1	Ligand/Ion	POTASSIUM ION
3	P6G	3	Ligand/Ion	HEXAETHYLENE GLYCOL

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	K	-1	Ligand/Ion	POTASSIUM ION
3	P6G	3	Ligand/Ion	HEXAETHYLENE GLYCOL

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	K	-1	Ligand/Ion	POTASSIUM ION
3	P6G	2	Ligand/Ion	HEXAETHYLENE GLYCOL

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:106 , ASP A:113 , MET A:114 , LEU A:115 , GLU A:117 , GLY A:119 , ALA A:123 , GLN A:262 , ARG A:270 , TYR A:302 , CL A:343	BINDING SITE FOR RESIDUE P6G A 341
2	AC2	SOFTWARE	HOH A:410	BINDING SITE FOR RESIDUE K A 342
3	AC3	SOFTWARE	ARG A:82 , ARG A:132 , P6G A:341	BINDING SITE FOR RESIDUE CL A 343
4	AC4	SOFTWARE	ASP B:113 , MET B:114 , LEU B:115 , ARG B:270 , TYR B:302 , HOH B:346 , HOH B:357	BINDING SITE FOR RESIDUE P6G B 341
5	AC5	SOFTWARE	GLU B:117 , HOH B:350 , HOH B:404	BINDING SITE FOR RESIDUE K B 342
6	AC6	SOFTWARE	LYS B:16 , TYR B:40	BINDING SITE FOR RESIDUE K B 343
7	AC7	SOFTWARE	ASN B:316 , ILE B:318 , SER B:328 , HOH B:353	BINDING SITE FOR RESIDUE K B 344
8	AC8	SOFTWARE	HOH B:351	BINDING SITE FOR RESIDUE CL B 345

(no "SS Bond" information available for 3HW9)

(no "Cis Peptide Bond" information available for 3HW9)

(no "SAP(SNP)/Variant" information available for 3HW9)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GRAM_NEG_PORIN	PS00576	General diffusion Gram-negative porins signature.	OMPF_ECOLI	317-333	2	A:295-311 B:295-311

Biological Unit 1 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GRAM_NEG_PORIN	PS00576	General diffusion Gram-negative porins signature.	OMPF_ECOLI	317-333	3	A:295-311 -

Biological Unit 2 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GRAM_NEG_PORIN	PS00576	General diffusion Gram-negative porins signature.	OMPF_ECOLI	317-333	3	- B:295-311

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GRAM_NEG_PORIN	PS00576	General diffusion Gram-negative porins signature.	OMPF_ECOLI	317-333	2	A:295-311 B:295-311

(no "Exon" information available for 3HW9)

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:339
 aligned with OMPF_ECOLI | P02931 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:340
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362
           OMPF_ECOLI    23 AEIYNKDGNKVDLYGKAVGLHYFSKGNGENSYGGNGDMTYARLGFKGETQINSDLTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF 362
               SCOP domains d3hw9a_ A: Porin                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 3hw9A00 A:1-340 Porin                                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeeeeeeeeeeeee...-........ee..eeeeeeeeeee....eeeeeeeeeeee.............eeeeeeeeeee...eeeeeeeee..hhhhhh.....................eeeeeeeeeehhhhhh....eeeeeee..............eeeeeeeeee..eeeeeeeeeee.hhhhhh.......eeeeeeeeeeeee..eeeeeeeeeee...eeee....eeee..eeeeeeeeeee.....eeeeeeeeeeeeeee...eeeeeeeeeeeeeeee....eeeeeeeeee..............eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GRAM_NEG_PORIN   ----------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hw9 A   1 AEIYNKDGNKVDLYGKAVGLHYFSKG-GENSYGGNGDMTYARLGFKGETQINSDLTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF 340
                                    10        20     | |30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340
                                                    26 |                                                                                                                                                                                                                                                                                                                        
                                                      28

Chain B from PDB  Type:PROTEIN  Length:339
 aligned with OMPF_ECOLI | P02931 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:340
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362
           OMPF_ECOLI    23 AEIYNKDGNKVDLYGKAVGLHYFSKGNGENSYGGNGDMTYARLGFKGETQINSDLTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF 362
               SCOP domains d3hw9b_ B: Porin                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 3hw9B00 B:1-340 Porin                                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeeeeeeeeeeeee...-........ee..eeeeeeeeeee....eeeeeeeeeeee.............eeeeeeeeeee...eeeeeeeee..hhhhhh.....................eeeeeeeee.hhhhhhh...eeeeeee..............eeeeeeeeee..eeeeeeeeeee.hhhhhh.......eeeeeeeeeeeee..eeeeeeeeeee...eeee....eeee..eeeeeeeeeee.....eeeeeeeeeeeeeee...eeeeeeeeeeeeeeee....eeeeeeeeee..............eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GRAM_NEG_PORIN   ----------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hw9 B   1 AEIYNKDGNKVDLYGKAVGLHYFSKG-GENSYGGNGDMTYARLGFKGETQINSDLTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF 340
                                    10        20     | |30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340
                                                    26 |                                                                                                                                                                                                                                                                                                                        
                                                      28

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(

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Folds(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Transmembrane beta-barrels (143)

Superfamily: Porins (99)

Family: Porin (49)

Protein domain: Porin (40)

Escherichia coli, different sequences [TaxId: 562] (27)

1a	d3hw9a_	A:
1b	d3hw9b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Porin (92)

Homologous Superfamily: Porin (47)

Escherichia coli. Organism_taxid: 83333. Strain: k-12. (2)

1a	3hw9A00	A:1-340
1b	3hw9B00	B:1-340

(no "Pfam Domain" information available for 3HW9)

Asymmetric Unit(hide GO term definitions)

Chain A,B (OMPF_ECOLI | P02931)

molecular function
	GO:0042912	colicin transmembrane transporter activity	Enables the transfer of a colicin from one side of a membrane to the other. Colicins are a group of antibiotics produced by E. coli and related species that are encoded by a group of naturally occurring plasmids, e.g. Col E1.
	GO:0015238	drug transmembrane transporter activity	Enables the directed movement of a drug from one side of a membrane to the other. A drug is any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
	GO:0015075	ion transmembrane transporter activity	Enables the transfer of an ion from one side of a membrane to the other.
	GO:0015288	porin activity	Catalysis of the transfer of substances, sized less than 1000 Da, from one side of the membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria.
biological process
	GO:0043213	bacteriocin transport	The directed movement of a bacteriocin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Bacteriocins are a group of antibiotics produced by bacteria and are encoded by a group of naturally occurring plasmids, e.g. Col E1. Bacteriocins are toxic to bacteria closely related to the bacteriocin producing strain.
	GO:0006855	drug transmembrane transport	The process in which a drug is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
	GO:0034220	ion transmembrane transport	A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	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.
	GO:0046930	pore complex	Any small opening in a membrane that allows the passage of gases and/or liquids.

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	3hw9
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3hwb	SAME STRUCTURE AT 3.0A RESOLUTION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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