2WQV - JenaLib

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Title :   INTERNALIN DOMAIN OF LISTERIA MONOCYTOGENES INLB: RHOMBOHEDRAL CRYSTAL FORM

Authors :   H. H. Niemann, D. W. Heinz

Date :   27 Aug 09 (Deposition) - 10 Nov 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Hgf Receptor Ligand, Leucine-Rich Repeat, Lrr, C-Met Ligand, Cell Invasion, Virulence Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. M. Ferraris, E. Gherardi, Y. Di, D. W. Heinz, H. H. Niemann
Ligand-Mediated Dimerization Of The Met Receptor Tyrosine Kinase By The Bacterial Invasion Protein Inlb.
J. Mol. Biol. V. 395 522 2010
PubMed-ID: 19900460 | Reference-DOI: 10.1016/J.JMB.2009.10.074

Molecule 1 - INTERNALIN B
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETM30
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	CODONPLUS
	Expression System Vector Type	:	PLASMID
	Fragment	:	INTERNALIN DOMAIN, RESIDUES 36-321
	Organism Scientific	:	LISTERIA MONOCYTOGENES
	Organism Taxid	:	169963
	Strain	:	EGD-E

		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 (2, 6)

No.	Name	Count	Type	Full Name
1	PG4	2	Ligand/Ion	TETRAETHYLENE GLYCOL
2	PGE	4	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL
2	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL
2	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:301 , ALA A:309 , ARG A:310 , ASN B:158 , THR B:180 , ARG B:184 , ASP B:263	BINDING SITE FOR RESIDUE PG4 A1321
2	AC2	SOFTWARE	ASN A:158 , ARG A:184 , ASP A:263 , ARG B:310	BINDING SITE FOR RESIDUE PG4 B1321
3	AC3	SOFTWARE	PRO A:269 , GLU A:270 , ILE A:272 , TYR A:278 , PRO B:269 , GLU B:270 , ILE B:271 , ILE B:272 , ASP B:277 , TYR B:278	BINDING SITE FOR RESIDUE PGE B1322
4	AC4	SOFTWARE	ASN A:76 , ASP A:79 , ASN A:99	BINDING SITE FOR RESIDUE PGE A1322
5	AC5	SOFTWARE	LYS A:145 , GLU A:167 , ASN B:212 , VAL B:234	BINDING SITE FOR RESIDUE PGE A1323
6	AC6	SOFTWARE	ASN A:212 , LYS B:145 , GLN B:165 , GLU B:167	BINDING SITE FOR RESIDUE PGE B1323

(no "SS Bond" information available for 2WQV)

Asymmetric Unit

No.	Residues
1	Lys A:280	-	Pro A:281
2	Lys B:280	-	Pro B:281

(no "SAP(SNP)/Variant" information available for 2WQV)

Asymmetric Unit (1, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LRR	PS51450	Leucine-rich repeat profile.	INLB_LISMO	99-120 121-142 143-164 165-186 187-208 209-230	12	A:99-120 B:99-120 A:121-142 B:121-142 A:143-164 B:143-164 A:165-186 B:165-186 A:187-208 B:187-208 A:209-230 B:209-230

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LRR	PS51450	Leucine-rich repeat profile.	INLB_LISMO	99-120 121-142 143-164 165-186 187-208 209-230	6	A:99-120 - A:121-142 - A:143-164 - A:165-186 - A:187-208 - A:209-230 -

Biological Unit 2 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LRR	PS51450	Leucine-rich repeat profile.	INLB_LISMO	99-120 121-142 143-164 165-186 187-208 209-230	6	- B:99-120 - B:121-142 - B:143-164 - B:165-186 - B:187-208 - B:209-230

(no "Exon" information available for 2WQV)

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:280
 aligned with INLB_LISMO | P25147 from UniProtKB/Swiss-Prot  Length:630

    Alignment length:284
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316    
           INLB_LISMO    37 TITVPTPIKQIFSDDAFAETIKDNLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVTKLFLNGNKLTDIKPLANLKNLGWLFLDENKVKDLSSLKDLKKLKSLSLEHNGISDINGLVHLPQLESLYLGNNKITDITVLSRLTKLDTLSLEDNQISDIVPLAGLTKLQNLYLSKNHISDLRALAGLKNLDVLELFSQECLNKPINHQSNLVVPNTVKNTDGSLVTPEIISDDGDYEKPNVKWHLPEFTNEVSFIFYQPVTIGKAKARFHGRVTQPLK 320
               SCOP domains d2wqva1 A:37-240 automated matches                                                                                                                                                                          d2wqva2 A:241-320 automated matches                                              SCOP domains
               CATH domains 2wqvA01 A:37-245 Ribonuclease Inhibitor                                                                                                                                                                          2wqvA02 A:246-320  [code=2.60.40.1220, no     name defined]                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eehhhhh.hhhhhhhhhhhh.......eehhhhhhh..eee...................eee........hhhhhhh.....ee.......hhhhhh......eee...................eee........hhhhhhh....eee........hhhhh......eee........hhhhh......eee.....ee........eeeee............eeee.....ee..eeeee.----.eeeeee.eeee....eeee...eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------LRR  PDB: A:99-120    LRR  PDB: A:121-142   LRR  PDB: A:143-164   LRR  PDB: A:165-186   LRR  PDB: A:187-208   LRR  PDB: A:209-230   ------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wqv A  37 TITVPTPIKQIFSDDAFAETIKDNLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVTKLFLNGNKLTDIKPLANLKNLGWLFLDENKVKDLSSLKDLKKLKSLSLEHNGISDINGLVHLPQLESLYLGNNKITDITVLSRLTKLDTLSLEDNQISDIVPLAGLTKLQNLYLSKNHISDLRALAGLKNLDVLELFSQECLNKPINHQSNLVVPNTVKNTDGSLVTPEIISDDGDYEKPNVKWHL----NEVSFIFYQPVTIGKAKARFHGRVTQPLK 320
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286|    | 296       306       316    
                                                                                                                                                                                                                                                                                    287  292

Chain B from PDB  Type:PROTEIN  Length:284
 aligned with INLB_LISMO | P25147 from UniProtKB/Swiss-Prot  Length:630

    Alignment length:284
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316    
           INLB_LISMO    37 TITVPTPIKQIFSDDAFAETIKDNLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVTKLFLNGNKLTDIKPLANLKNLGWLFLDENKVKDLSSLKDLKKLKSLSLEHNGISDINGLVHLPQLESLYLGNNKITDITVLSRLTKLDTLSLEDNQISDIVPLAGLTKLQNLYLSKNHISDLRALAGLKNLDVLELFSQECLNKPINHQSNLVVPNTVKNTDGSLVTPEIISDDGDYEKPNVKWHLPEFTNEVSFIFYQPVTIGKAKARFHGRVTQPLK 320
               SCOP domains d2wqvb1 B:37-240 automated matches                                                                                                                                                                          d2wqvb2 B:241-320 automated matches                                              SCOP domains
               CATH domains 2wqvB01 B:37-245 Ribonuclease Inhibitor                                                                                                                                                                          2wqvB02 B:246-320  [code=2.60.40.1220, no name defined]                     CATH domains
           Pfam domains (1) Internalin_N-2wqvB07   --------------------------------------------------------------------------------------------------------LRR_4-2wqvB01 B:164-206                    LRR_6-2wqvB05 B:207-233    ------------------------------LRR_adjacent-2wqvB09 B:264-320                            Pfam domains (1)
           Pfam domains (2) Internalin_N-2wqvB08   --------------------------------------------------------------------------------------------------------LRR_4-2wqvB02 B:164-206                    LRR_6-2wqvB06 B:207-233    ------------------------------LRR_adjacent-2wqvB10 B:264-320                            Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------LRR_4-2wqvB03 B:164-206                    ------------------------------------------------------------------------------------------------------------------ Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------------------------------LRR_4-2wqvB04 B:164-206                    ------------------------------------------------------------------------------------------------------------------ Pfam domains (4)
         Sec.struct. author .....eehhhhh.hhhhhhhhhhhh.......eehhhhhhh..eee...................eee........hhhhhhh.....ee.......hhhhhh......eee...................eee........hhhhhhh....eee........hhhhh......eee........hhhhh......eee.....ee...ee...eeeee.....................ee..eeeee.............eeee....eeee...eeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------LRR  PDB: B:99-120    LRR  PDB: B:121-142   LRR  PDB: B:143-164   LRR  PDB: B:165-186   LRR  PDB: B:187-208   LRR  PDB: B:209-230   ------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wqv B  37 TITVPTPIKQIFSDDAFAETIKDNLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVTKLFLNGNKLTDIKPLANLKNLGWLFLDENKVKDLSSLKDLKKLKSLSLEHNGISDINGLVHLPQLESLYLGNNKITDITVLSRLTKLDTLSLEDNQISDIVPLAGLTKLQNLYLSKNHISDLRALAGLKNLDVLELFSQECLNKPINHQSNLVVPNTVKNTDGSLVTPEIISDDGDYEKPNVKWHLPEFTNEVSFIFYQPVTIGKAKARFHGRVTQPLK 320
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316

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

Clans(

)

Families(

)

Organisms( (-)

)

Clan: LRR (77)

Family: LRR_4 (28)

Listeria monocytogenes (18)

1a	LRR_4-2wqvB01	B:164-206
1b	LRR_4-2wqvB02	B:164-206
1c	LRR_4-2wqvB03	B:164-206
1d	LRR_4-2wqvB04	B:164-206

Family: LRR_6 (24)

Listeria monocytogenes (10)

2a	LRR_6-2wqvB05	B:207-233
2b	LRR_6-2wqvB06	B:207-233

Clan: no clan defined [family: Internalin_N] (18)

Family: Internalin_N (18)

Listeria monocytogenes (18)

3a	Internalin_N-2wqvB07	B:37-59
3b	Internalin_N-2wqvB08	B:37-59

Clan: no clan defined [family: LRR_adjacent] (15)

Family: LRR_adjacent (15)

Listeria monocytogenes (15)

4a	LRR_adjacent-2wqvB09	B:264-320
4b	LRR_adjacent-2wqvB10	B:264-320

Asymmetric Unit(hide GO term definitions)

Chain A,B (INLB_LISMO | P25147)

molecular function
	GO:0005515		protein binding		Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).

Asymmetric Unit
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	Cis Peptide Bonds
		Lys A:280 - Pro A:281	[ RasMol ]
		Lys B:280 - Pro B:281	[ RasMol ]

Biological Units
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	2wqv
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1d0b	INTERNALIN B LEUCINE RICH REPEAT DOMAIN
1h6t	INTERNALIN B: CRYSTAL STRUCTURE OF FUSED N- TERMINAL DOMAINS.
1m9s	CRYSTAL STRUCTURE OF INTERNALIN B (INLB), A LISTERIAMONOCYTOGENES VIRULENCE PROTEIN CONTAINING SH3-LIKEDOMAINS.
1otm	CALCIUM-BINDING MUTANT OF THE INTERNALIN B LRR DOMAIN
1otn	CALCIUM-BINDING MUTANT OF THE INTERNALIN B LRR DOMAIN
1oto	CALCIUM-BINDING MUTANT OF THE INTERNALIN B LRR DOMAIN
2uzx	STRUCTURE OF THE HUMAN RECEPTOR TYROSINE KINASE MET IN COMPLEX WITH THE LISTERIA MONOCYTOGENES INVASION PROTEIN INLB: CRYSTAL FORM I
2uzy	STRUCTURE OF THE HUMAN RECEPTOR TYROSINE KINASE MET IN COMPLEX WITH THE LISTERIA MONOCYTOGENES INVASION PROTEIN INLB: LOW RESOLUTION, CRYSTAL FORM II
2wqu	INTERNALIN DOMAIN OF LISTERIA MONOCYTOGENES INLB: TRICLINIC CRYSTAL FORM
2wqw	DOUBLE-DISULFIDE CROSS-LINKED CRYSTAL DIMER OF THE LISTERIA MONOCYTOGENES INLB INTERNALIN DOMAIN
2wqx	INLB321_4R: S199R, D200R, G206R, A227R, C242A MUTANT OF THE LISTERIA MONOCYTOGENES INLB INTERNALIN DOMAIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 12)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 4)

CATH Domains (2, 4)

Pfam Domains (4, 10)

Gene Ontology (1, 1)

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