2WQW - JenaLib

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Title :   DOUBLE-DISULFIDE CROSS-LINKED CRYSTAL DIMER OF THE LISTERIA MONOCYTOGENES INLB INTERNALIN DOMAIN

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

Date :   27 Aug 09 (Deposition) - 10 Nov 09 (Release) - 09 Feb 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.24

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

Keywords :   Hgf Receptor Ligand, Leucine-Rich Repeat, 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 CODON PLUS (DE3)
	Expression System Taxid	:	469008
	Fragment	:	INTERNALIN DOMAIN, RESIDUES 36-321
	Mutation	:	YES
	Organism Scientific	:	LISTERIA MONOCYTOGENES
	Organism Taxid	:	169963
	Other Details	:	RESIDUES 36-321 OF LISTERIA MONOCYTOGENES INLB CROSS-LINKED INTO DIMERS BY TWO INTERMOLECULAR DISULFIDE BONDS BETWEEN C206 AND C227
	Strain	:	EGD-E
	Synonym	:	INLB

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 9)

No.	Name	Count	Type	Full Name
1	PEG	9	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (1, 12)

No.	Name	Count	Type	Full Name
1	PEG	12	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	PEG	6	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:99 , HOH A:2064 , HOH A:2065 , PHE B:104	BINDING SITE FOR RESIDUE PEG A1322
2	AC2	SOFTWARE	LYS A:120 , ASN A:121 , LYS A:143 , PHE B:126 , ASP B:128 , SER B:148 , HOH B:2019 , HOH B:2074	BINDING SITE FOR RESIDUE PEG B1322
3	AC3	SOFTWARE	ASP A:128 , SER A:148 , GLU A:150 , ASN B:121 , LYS B:143	BINDING SITE FOR RESIDUE PEG A1323
4	AC4	SOFTWARE	THR A:37 , ASN B:85	BINDING SITE FOR RESIDUE PEG B1323
5	AC5	SOFTWARE	LYS A:142 , LYS A:145	BINDING SITE FOR RESIDUE PEG A1324
6	AC6	SOFTWARE	ASN B:76 , SER B:77 , ASP B:79 , ASN B:99 , HOH B:2017 , HOH B:2075 , HOH B:2076	BINDING SITE FOR RESIDUE PEG B1324
7	AC7	SOFTWARE	PRO A:269 , GLU A:270 , ILE A:272 , PRO B:269 , GLU B:270 , ILE B:272 , HOH B:2077	BINDING SITE FOR RESIDUE PEG B1325
8	AC8	SOFTWARE	ASN A:85 , THR B:37 , TYR B:96	BINDING SITE FOR RESIDUE PEG B1326
9	AC9	SOFTWARE	ASP B:222 , THR B:258 , LYS B:260	BINDING SITE FOR RESIDUE PEG B1327

Asymmetric Unit

No.	Residues
1	A:206	-	A:227
2	B:206	-	B:227

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 2WQW)

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, 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	- B:99-120 - B:121-142 - B:143-164 - B:165-186 - B:187-208 - B:209-230

Biological Unit 2 (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 - A:121-142 - A:143-164 - A:165-186 - A:187-208 - A:209-230 -

(no "Exon" information available for 2WQW)

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:286
 aligned with INLB_LISMO | P25147 from UniProtKB/Swiss-Prot  Length:630

    Alignment length:286
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315      
           INLB_LISMO    36 ETITVPTPIKQIFSDDAFAETIKDNLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVTKLFLNGNKLTDIKPLANLKNLGWLFLDENKVKDLSSLKDLKKLKSLSLEHNGISDINGLVHLPQLESLYLGNNKITDITVLSRLTKLDTLSLEDNQISDIVPLAGLTKLQNLYLSKNHISDLRALAGLKNLDVLELFSQECLNKPINHQSNLVVPNTVKNTDGSLVTPEIISDDGDYEKPNVKWHLPEFTNEVSFIFYQPVTIGKAKARFHGRVTQPLKE 321
               SCOP domains d2wqwa1 A:36-240 automated matches                                                                                                                                                                           d2wqwa2 A:241-321 automated matches                                               SCOP domains
               CATH domains 2wqwA01 A:36-245 Ribonuclease Inhibitor                                                                                                                                                                           2wqwA02 A:246-321  [code=2.60.40.1220, no name defined]                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eehhhhh.hhhhhhhhhhhh.......eehhhhhh...eee...................eee........hhhhhhh.....ee........hhhhh......eee...................eee........hhhhhhh....eee........hhhhhhh....eee........hhhhh......eee.....ee...ee...eeeee.....................ee..eeeee.............eeee....eeee...eeeeee. 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
                 2wqw A  36 ETITVPTPIKQIFSDDAFAETIKDNLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVTKLFLNGNKLTDIKPLANLKNLGWLFLDENKVKDLSSLKDLKKLKSLSLEHNGISDINGLVHLPQLESLYLGNNKITDITVLSRLTKLDTLSLEDNQISDIVPLACLTKLQNLYLSKNHISDLRALCGLKNLDVLELFSQEALNKPINHQSNLVVPNTVKNTDGSLVTPEIISDDGDYEKPNVKWHLPEFTNEVSFIFYQPVTIGKAKARFHGRVTQPLKE 321
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315

Chain B from PDB  Type:PROTEIN  Length:286
 aligned with INLB_LISMO | P25147 from UniProtKB/Swiss-Prot  Length:630

    Alignment length:286
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315      
           INLB_LISMO    36 ETITVPTPIKQIFSDDAFAETIKDNLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVTKLFLNGNKLTDIKPLANLKNLGWLFLDENKVKDLSSLKDLKKLKSLSLEHNGISDINGLVHLPQLESLYLGNNKITDITVLSRLTKLDTLSLEDNQISDIVPLAGLTKLQNLYLSKNHISDLRALAGLKNLDVLELFSQECLNKPINHQSNLVVPNTVKNTDGSLVTPEIISDDGDYEKPNVKWHLPEFTNEVSFIFYQPVTIGKAKARFHGRVTQPLKE 321
               SCOP domains d2wqwb1 B:36-240 automated matches                                                                                                                                                                           d2wqwb2 B:241-321 automated matches                                               SCOP domains
               CATH domains 2wqwB01 B:36-245 Ribonuclease Inhibitor                                                                                                                                                                           2wqwB02 B:246-321  [code=2.60.40.1220, no name defined]                      CATH domains
           Pfam domains (1) Internalin_N-2wqwB07    --------------------------------------------------------------------------------------------------------LRR_4-2wqwB01 B:164-206                    LRR_6-2wqwB05 B:207-233    ------------------------------LRR_adjacent-2wqwB09 B:264-321                             Pfam domains (1)
           Pfam domains (2) Internalin_N-2wqwB08    --------------------------------------------------------------------------------------------------------LRR_4-2wqwB02 B:164-206                    LRR_6-2wqwB06 B:207-233    ------------------------------LRR_adjacent-2wqwB10 B:264-321                             Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------LRR_4-2wqwB03 B:164-206                    ------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------LRR_4-2wqwB04 B:164-206                    ------------------------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ......eehhhhh.hhhhhhhhhhhh.......eehhhhhh...eee...................eee........hhhhhhh.....ee........hhhhh......eee...................eee........hhhhhhh....eee........hhhhhhh....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
                 2wqw B  36 ETITVPTPIKQIFSDDAFAETIKDNLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVTKLFLNGNKLTDIKPLANLKNLGWLFLDENKVKDLSSLKDLKKLKSLSLEHNGISDINGLVHLPQLESLYLGNNKITDITVLSRLTKLDTLSLEDNQISDIVPLACLTKLQNLYLSKNHISDLRALCGLKNLDVLELFSQEALNKPINHQSNLVVPNTVKNTDGSLVTPEIISDDGDYEKPNVKWHLPEFTNEVSFIFYQPVTIGKAKARFHGRVTQPLKE 321
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315

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_4-2wqwB01	B:164-206
1b	LRR_4-2wqwB02	B:164-206
1c	LRR_4-2wqwB03	B:164-206
1d	LRR_4-2wqwB04	B:164-206

Family: LRR_6 (24)

Listeria monocytogenes (10)

2a	LRR_6-2wqwB05	B:207-233
2b	LRR_6-2wqwB06	B:207-233

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

Family: Internalin_N (18)

Listeria monocytogenes (18)

3a	Internalin_N-2wqwB07	B:36-59
3b	Internalin_N-2wqwB08	B:36-59

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

Family: LRR_adjacent (15)

Listeria monocytogenes (15)

4a	LRR_adjacent-2wqwB09	B:264-321
4b	LRR_adjacent-2wqwB10	B:264-321

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 ]

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	2wqw
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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
2wqv	INTERNALIN DOMAIN OF LISTERIA MONOCYTOGENES INLB: RHOMBOHEDRAL CRYSTAL FORM
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 (1, 9)

Sites (9, 9)

SS Bonds (2, 2)

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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