4QQ1 - JenaLib

Title :   CRYSTAL STRUCTURE OF THE ISOTYPE 1 TRANSFERRIN BINDING PROTEIN B (TBPB) FROM SEROGROUP B NEISSERIA MENINGITIDIS

Authors :   C. Calmettes, T. F. Moraes

Date :   26 Jun 14 (Deposition) - 01 Apr 15 (Release) - 01 Jul 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.33

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

Keywords :   Vaccine Candidate, Transferrin Receptor, Iron Acquisition, Surface Lipoprotein, Host-Pathogen Interaction, Iron Piracy, Transferrin Binding, Outer-Membrane, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Adamiak, C. Calmettes, T. F. Moraes, A. B. Schryvers
Patterns Of Structural And Sequence Variation Within Isotyp Lineages Of The Neisseria Meningitidis Transferrin Receptor System.
Microbiologyopen V. 4 491 2015
PubMed-ID: 25800619 | Reference-DOI: 10.1002/MBO3.254

Compounds

Molecule 1 - TRANSFERRIN-BINDING PROTEIN 2
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUED 58-599
	Gene	:	TBPB, TBP2
	Organism Scientific	:	NEISSERIA MENINGITIDIS SEROGROUP B
	Organism Taxid	:	491
	Strain	:	SEROGROUP B, STRAIN B16B6
	Synonym	:	TBP-2

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 11)

Asymmetric Unit (3, 11)

No.	Name	Count	Type	Full Name
1	CS	8	Ligand/Ion	CESIUM ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CS	-1	Ligand/Ion	CESIUM ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CS	-1	Ligand/Ion	CESIUM ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	CS	-1	Ligand/Ion	CESIUM ION
2	GOL	-1	Ligand/Ion	GLYCEROL
3	SO4	1	Ligand/Ion	SULFATE ION

Sites (10, 10)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:191 , ASP A:193 , LYS A:194	BINDING SITE FOR RESIDUE CS A 601
02	AC2	SOFTWARE	LYS A:279 , SER A:290	BINDING SITE FOR RESIDUE CS A 602
03	AC3	SOFTWARE	GLU A:203 , ARG A:243	BINDING SITE FOR RESIDUE CS A 604
04	AC4	SOFTWARE	ASN A:84 , PHE A:119 , VAL A:122 , ARG A:123 , HOH A:714	BINDING SITE FOR RESIDUE GOL A 605
05	AC5	SOFTWARE	GLY B:191 , ASP B:193	BINDING SITE FOR RESIDUE CS B 601
06	AC6	SOFTWARE	SER B:290	BINDING SITE FOR RESIDUE CS B 602
07	AC7	SOFTWARE	LEU A:206 , ILE A:254 , GLN B:253 , THR B:257	BINDING SITE FOR RESIDUE GOL B 603
08	AC8	SOFTWARE	GLY C:191 , ASP C:193 , LYS C:194	BINDING SITE FOR RESIDUE CS C 601
09	AC9	SOFTWARE	ARG C:258	BINDING SITE FOR RESIDUE CS C 602
10	BC1	SOFTWARE	TYR C:116 , LYS C:168	BINDING SITE FOR RESIDUE SO4 C 603

SS Bonds (3, 3)

Cis Peptide Bonds (23, 23)

Asymmetric Unit

No.	Residues
1	Glu A:107	-	Asp A:108
2	Asn A:138	-	Asn A:139
3	Gly A:351	-	Glu A:352
4	Lys A:384	-	Ala A:385
5	Cys A:401	-	Cys A:402
6	Pro A:429	-	Val A:430
7	Asn A:453	-	Gly A:454
8	Gly A:454	-	Thr A:455
9	Gly B:97	-	Ser B:98
10	Glu B:107	-	Asp B:108
11	Asn B:138	-	Asn B:139
12	Ala B:281	-	Thr B:282
13	Thr B:350	-	Gly B:351
14	Gly B:351	-	Glu B:352
15	Cys B:401	-	Cys B:402
16	Ala B:435	-	Arg B:436
17	Glu C:107	-	Asp C:108
18	Gly C:351	-	Glu C:352
19	Cys C:401	-	Cys C:402
20	Ala C:434	-	Ala C:435
21	Asn C:453	-	Gly C:454
22	Gly C:454	-	Thr C:455
23	Asn C:526	-	Ser C:527

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:521
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...............ee..hhh.eeee.......hhhhhhhhhhhh....ee..................eeeeeeee...eee....eee...eeeeeeee.....eee..eeeeeeeeeeee.ee........hhhhh......hhhhh...................eeeeeee....eeeeee....................eeeeeee...eeeeeeee...............eeeeeeeee.....eeeeeee.....eeeeeeee........eee.eeeeee......eee........eee....eee...........eeeee....eeeee......eeeeeee......eeeeee...hhhhhhh......eeeeeeeeee....eee.......eeeeee.....eeeeeee........eeeeeeee..eeeeeee.....ee..........ee..eeeeeeeee.....eeeeeeee.....eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qq1 A  43 GAAYGFAVKLPRRNAHFNPKYKEKHKPLGSMDWKKLQRGEPNSFSERDELEKKRGSSELIESKWEDGQSRVVGYTNFTYVRSGYVYLNKNNIDIKNNIVLFGPDGYLYYKGKEPSKELPSEKITYKGTWDYVTDAMEKQRFEGLGSAAGGDKSGALSALEEGVLRNQAEASSGHTDFGMTSEFEVDFSDKTIKGTLYRNNRITQNNSENKQIKTTRYTIQATLHGNRFKGKALAADKGATNGSHPFISDSDSLEGGFYGPKGEELAGKFLSNDNKVAAVFGAKQKDAAGPATETVIDAYRITGEEFKKEQIDSFGDVKKLLVDGVELSLLPSEGNKAAFQHEIEQNGVKATVCCSNLDYMSFGKLSKENKDDMFLQGVRTPVSDVAARTEANAKYRGTWYGYIANGTSWSGEASNGGNRAEFDVDFSTKKISGTLTAKDRTSPAFTITAMIKDNGFSGVAKTGENGFALDPQNTGNSHYTHIEATVSGGFYGKNAIEMGGSFSFPGNQEKASVVFGAKRQQ 576
                                    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     ||338       348       358       368       378       388       398       408       418       428       438       448       458    || 470       480       490       500       510       520       530       540       550      |565       575 
                                                                                                                                                                                                                                                                                                                       328|                                                                                                                             463|                                                                                        557|             
                                                                                                                                                                                                                                                                                                                        335                                                                                                                              466                                                                                         563

Chain B from PDB  Type:PROTEIN  Length:485
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...............ee..hhhhheee.......hhhhhhhhhhh.....ee..................eeeeeeee...eee....eee...eeeeeeee.....eee..eeeeeeeeeeee.ee...................hhhhh...............eeeeeee....eeeeeeeee....eeeeeeeeeee...eeeeeeee...............eeeeeeeee.....eeeeeee.....eeeeeeee......eee.eeeeee......eee........eee....eee....eeee....eeeee......eeeeeee.....eeeeeee...hhhhhh.......eeeeeeeeee...eeee.........eeeeeee....eeeeeee........eeeeeeee..eeeeeee.............eeeeeeeee.....eeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qq1 B  42 SGAAYGFAVKLPRRNAHFNPKYKEKHKPLGSMDWKKLQRGEPNSFSERDELEKKRGSSELIESKWEDGQSRVVGYTNFTYVRSGYVYLNKNNIDIKNNIVLFGPDGYLYYKGKEPSKELPSEKITYKGTWDYVTDAMEKQRFEGLGSAAGGDKSGALSALEEGVLRNQAGHTDFGMTSEFEVDFSDKTIKGTLYRNNRQIKTTRYTIQATLHGNRFKGKALAADKGATNGSHPFISDSDSLEGGFYGPKGEELAGKFLSNDNKVAAVFGAKQKDKPATETVIDAYRITGEEFKKEQIDSFGDVKKLLVDGVELSLLFQHEIEQNGVKATVCCSNLDYMSFGKLSKENKDDMFLQGVRTPVSDVAARTEANAKYRGTWYGYIANGTSWSGEASNQEGGNRAEFDVDFSTKKISGTLTAKDRTSPAFTITAMIKDNGFSGVAKTGENGFASHYTHIEATVSGGFYGKNAIEMGGSFSFASVVFGAKR 574
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       215       225       235       254       264       274       284       294       304       314       324    || 342       352       362       372     ||390       400       410       420       430       440       450       460       470       480       490       500       510       528       538       548     ||569     
                                                                                                                                                                                                  210|                         243|                                                                         329|                                     378|                                                                                                                                518|                        554|        
                                                                                                                                                                                                   215                          253                                                                          338                                      387                                                                                                                                 527                         566

Chain C from PDB  Type:PROTEIN  Length:515
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...............ee..hhhhheee.......hhhhhhhhhhh.....ee..................eeeeeeee...eee..eee...eeeeeeee.....eee..eeeeeeeeeeee.ee...................hhhhh...................eeeeeee....eeeeeeeee..........eeeeeeeeeee...eeeeeeee...............eeeeeeeee.....eeeeeee.....eeeeeeee.........eee.eeeeee......eee........eee....eee.......eeee....eeeee......eeeeeee.....eeeeeee..hhhhhh........eeeeeeeeee....eee.........eeeeee.....eeeeeee........eeeeeeee..eeeeeee.....................eeeeeeeee.....eeeeeeee......eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qq1 C  42 SGAAYGFAVKLPRRNAHFNPKYKEKHKPLGSMDWKKLQRGEPNSFSERDELEKKRGSSELIESKWEDGQSRVVGYTNFTYVRSGYVYLNKNNIDINIVLFGPDGYLYYKGKEPSKELPSEKITYKGTWDYVTDAMEKQRFEGLGSAAGGDKSGALSALEEGVLRNQAEASSGHTDFGMTSEFEVDFSDKTIKGTLYRNNRITQENKQIKTTRYTIQATLHGNRFKGKALAADKGATNGSHPFISDSDSLEGGFYGPKGEELAGKFLSNDNKVAAVFGAKQKDKAAGPATETVIDAYRITGEEFKKEQIDSFGDVKKLLVDGVELSLLPAAFQHEIEQNGVKATVCCSNLDYMSFGKLSKENKDDMFLQGVRTPVSDVAARTEANAKYRGTWYGYIANGTSWSGEASNQEGGNRAEFDVDFSTKKISGTLTAKDRTSPAFTITAMIKDNGFSGVAKTGENGFALDPQNTGNSHYTHIEATVSGGFYGKNAIEMGGSFSFPEGKQEKASVVFGAKRQ 575
                                    51        61        71        81        91       101       111       121       131    || 143       153       163       173       183       193       203       213       223       233       243  ||   256       266       276       286       296       306       316       326  ||   341       351       361       371       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       560       570     
                                                                                                                        136|                                                                                                        246|                                                                            329|                                         379|                                                                                                                                                                       555|               
                                                                                                                         139                                                                                                         250                                                                             335                                          385                                                                                                                                                                        560

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (3, 3)

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	Cis Peptide Bonds
		Ala B:281 - Thr B:282	[ RasMol ]
		Ala B:435 - Arg B:436	[ RasMol ]
		Ala C:434 - Ala C:435	[ RasMol ]
		Asn A:138 - Asn A:139	[ RasMol ]
		Asn A:453 - Gly A:454	[ RasMol ]
		Asn B:138 - Asn B:139	[ RasMol ]
		Asn C:453 - Gly C:454	[ RasMol ]
		Asn C:526 - Ser C:527	[ RasMol ]
		Cys A:401 - Cys A:402	[ RasMol ]
		Cys B:401 - Cys B:402	[ RasMol ]
		Cys C:401 - Cys C:402	[ RasMol ]
		Glu A:107 - Asp A:108	[ RasMol ]
		Glu B:107 - Asp B:108	[ RasMol ]
		Glu C:107 - Asp C:108	[ RasMol ]
		Gly A:351 - Glu A:352	[ RasMol ]
		Gly A:454 - Thr A:455	[ RasMol ]
		Gly B:351 - Glu B:352	[ RasMol ]
		Gly B:97 - Ser B:98	[ RasMol ]
		Gly C:351 - Glu C:352	[ RasMol ]
		Gly C:454 - Thr C:455	[ RasMol ]
		Lys A:384 - Ala A:385	[ RasMol ]
		Pro A:429 - Val A:430	[ RasMol ]
		Thr B:350 - Gly B:351	[ RasMol ]

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