3CX3 - JenaLib

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Title :   CRYSTAL STRUCTURE ANALYSIS OF THE STREPTOCOCCUS PNEUMONIAE ADCAII PROTEIN

Authors :   E. Loisel, C. Durmort, L. Jacquamet

Date :   23 Apr 08 (Deposition) - 05 Aug 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Zinc-Binding, Lipoprotein, Transport, Lipid Binding Protein, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Loisel, L. Jacquamet, L. Serre, C. Bauvois, J. L. Ferrer, T. Vernet, A. M. Di Guilmi, C. Durmort
Adcaii, A New Pneumococcal Zn-Binding Protein Homologous With Abc Transporters: Biochemical And Structural Analysis.
J. Mol. Biol. V. 381 594 2008
PubMed-ID: 18632116 | Reference-DOI: 10.1016/J.JMB.2008.05.068
(for further references see the PDB file header)

Molecule 1 - LIPOPROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PLIM01
	Expression System Strain	:	BL21(DE3)
	Expression System Vector Type	:	PLASMID
	Gene	:	LMB, SPR0906
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE
	Organism Taxid	:	171101
	Strain	:	R6
	Synonym	:	ADCAII, ADHESION LIPOPROTEIN

		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 (3, 14)

No.	Name	Count	Type	Full Name
1	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
2	NA	2	Ligand/Ion	SODIUM ION
3	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	MSE	5	Mod. Amino Acid	SELENOMETHIONINE
2	NA	-1	Ligand/Ion	SODIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 5)

No.	Name	Count	Type	Full Name
1	MSE	5	Mod. Amino Acid	SELENOMETHIONINE
2	NA	-1	Ligand/Ion	SODIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:173 , THR A:176	BINDING SITE FOR RESIDUE NA A 313
2	AC2	SOFTWARE	HIS A:71 , HIS A:147 , HIS A:211 , ILE A:231 , GLU A:286	BINDING SITE FOR RESIDUE ZN A 314
3	AC3	SOFTWARE	HIS B:71 , HIS B:147 , HIS B:211 , ILE B:231 , GLU B:286	BINDING SITE FOR RESIDUE ZN B 312

(no "SS Bond" information available for 3CX3)

Asymmetric Unit

No.	Residues
1	Ser A:238	-	Pro A:239
2	Asn B:291	-	Asp B:292

(no "SAP(SNP)/Variant" information available for 3CX3)

(no "PROSITE Motif" information available for 3CX3)

(no "Exon" information available for 3CX3)

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:264
 aligned with Q8DQ09_STRR6 | Q8DQ09 from UniProtKB/TrEMBL  Length:311

    Alignment length:277
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       
         Q8DQ09_STRR6    34 TGKGMKIVTSFYPIYAMVKEVSGDLNDVRMIQSSSGIHSFEPSANDIAAIYDADVFVYHSHTLESWAGSLDPNLKKSKVKVLEASEGMTLERVPGLEDVEAGDGVDEKTLYDPHTWLDPEKAGEEAQIIADKLSEVDSEHKETYQKNAQAFIKKAQELTKKFQPKFEKATQKTFVTQHTAFSYLAKRFGLNQLGIAGISPEQEPSPRQLTEIQEFVKTYKVKTIFTESNASSKVAETLVKSTGVGLKTLNPLESDPQNDKTYLENLEENMSILAEEL 310
               SCOP domains d3cx3a_ A: automated matches                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3cx3A01 A:34-202 Nitrogenase molybdenum iron protein domain                                                                                                              3cx3A02 A:203-310 Nitrogenase molybdenum iron protein domain                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.hhhhhhhhhhhhh...eeee............hhhhhhhhhhh.eeee.....................eeee............-------------.....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhh...eeeee.........hhhhhhhhhhhhhh....eee.....hhhhhhhhh.....eee............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cx3 A  34 TGKGmKIVTSFYPIYAmVKEVSGDLNDVRmIQSSSGIHSFEPSANDIAAIYDADVFVYHSHTLESWAGSLDPNLKKSKVKVLEASEGmTLERVPG-------------TLYDPHTWLDPEKAGEEAQIIADKLSEVDSEHKETYQKNAQAFIKKAQELTKKFQPKFEKATQKTFVTQHTAFSYLAKRFGLNQLGIAGISPEQEPSPRQLTEIQEFVKTYKVKTIFTESNASSKVAETLVKSTGVGLKTLNPLESDPQNDKTYLENLEENmSILAEEL 310
                                |   43      | 53        63        73        83        93       103       113       123    |    -       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       
                                |          50-MSE       63-MSE                                                   121-MSE128           142                                                                                                                                                              303-MSE   
                               38-MSE

Chain B from PDB  Type:PROTEIN  Length:260
 aligned with Q8DQ09_STRR6 | Q8DQ09 from UniProtKB/TrEMBL  Length:311

    Alignment length:276
                                    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      
         Q8DQ09_STRR6    36 KGMKIVTSFYPIYAMVKEVSGDLNDVRMIQSSSGIHSFEPSANDIAAIYDADVFVYHSHTLESWAGSLDPNLKKSKVKVLEASEGMTLERVPGLEDVEAGDGVDEKTLYDPHTWLDPEKAGEEAQIIADKLSEVDSEHKETYQKNAQAFIKKAQELTKKFQPKFEKATQKTFVTQHTAFSYLAKRFGLNQLGIAGISPEQEPSPRQLTEIQEFVKTYKVKTIFTESNASSKVAETLVKSTGVGLKTLNPLESDPQNDKTYLENLEENMSILAEELK 311
               SCOP domains d3cx3b_ B: automated matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 3cx3B01 B:36-202 Nitrogenase molybdenum iron protein domain                                                                                                            3cx3B02 B:203-311 Nitrogenase molybdenum iron protein domain                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee.hhhhhhhhhhhhhhhheeee............hhhhhhhhhhh.eeee.....hhhhhh...........eee............-------------.....hhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhh..eeee..........hhhhhhhhhhhhhhhh..eeee....h--hhhhhhhhh..eeee........-...hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cx3 B  36 KGmKIVTSFYPIYAmVKEVSGDLNDVRmIQSSSGIHSFEPSANDIAAIYDADVFVYHSHTLESWAGSLDPNLKKSKVKVLEASEGmTLERVPG-------------TLYDPHTWLDPEKAGEEAQIIADKLSEVDSEHKETYQKNAQAFIKKAQELTKKFQPKFEKATQKTFVTQHTAFSYLAKRFGLNQLGIAGISPEQEPSPRQLTEIQEFVKTYKVKTIFTESNAS--VAETLVKSTGVGLKTLNPLESDP-NDKTYLENLEENmSILAEELK 311
                              |     45    |   55       |65        75        85        95       105       115     | 125  |      -      |145       155       165       175       185       195       205       215       225       235       245       255        |- |     275       285   | | 295       305      
                             38-MSE      50-MSE       63-MSE                                                   121-MSE128           142                                                                                                                       264  |                   289 |         303-MSE    
                                                                                                                                                                                                                                                                 267                     291

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(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Chelatase-like (149)

Superfamily: Helical backbone metal receptor (102)

Family: automated matches (30)

Protein domain: automated matches (30)

Streptococcus pneumoniae [TaxId: 171101] (1)

1a	d3cx3a_	A:
1b	d3cx3b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Nitrogenase molybdenum iron protein domain (45)

Streptococcus pneumoniae. Organism_taxid: 171101. Strain: r6. (1)

1a	3cx3B01	B:36-202
1b	3cx3A01	A:34-202
1c	3cx3A02	A:203-310
1d	3cx3B02	B:203-311

(no "Pfam Domain" information available for 3CX3)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q8DQ09_STRR6 | Q8DQ09)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0030001	metal ion transport	The directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0010043	response to zinc ion	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a zinc ion stimulus.
	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:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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	Cis Peptide Bonds
		Asn B:291 - Asp B:292	[ RasMol ]
		Ser A:238 - Pro A:239	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (3, 14)

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