3ZKA - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PNEUMOCOCCAL SURFACE ANTIGEN PSAA D280N IN THE METAL-BOUND, OPEN STATE

Authors :   R. M. Counago, M. P. Ween, M. Bajaj, J. Zuegg, M. A. Cooper, A. G. Mcewan, J B. Kobe, C. A. Mcdevitt

Date :   22 Jan 13 (Deposition) - 06 Nov 13 (Release) - 08 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

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

Keywords :   Metal Transport, Atp-Binding Cassette Transporters, Bacterial Adhesion, Carrier Proteins, Lipoproteins, Membrane Transport Proteins (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. M. Counago, M. P. Ween, S. L. Begg, M. Bajaj, J. Zuegg, M. L. O'Mara, M. A. Cooper, A. G. Mcewan, J. C. Paton, B. Kobe, C. A. Mcdevitt
Imperfect Coordination Chemistry Facilitates Metal Ion Release In The Psa Permease.
Nat. Chem. Biol. V. 10 35 2014
PubMed-ID: 24212134 | Reference-DOI: 10.1038/NCHEMBIO.1382
(for further references see the PDB file header)

Molecule 1 - MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	RESIDUES 32-309
	Mutation	:	YES
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE
	Organism Taxid	:	1313
	Synonym	:	PSAA, PNEUMOCOCCAL SURFACE ADHESIN A

		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, 4)

No.	Name	Count	Type	Full Name
1	MN	2	Ligand/Ion	MANGANESE (II) ION
2	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION
2	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION
2	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:139 , GLU A:205 , HOH A:2156 , HOH A:2157 , HOH A:2158 , HOH A:2204	BINDING SITE FOR RESIDUE MN A1310
2	AC2	SOFTWARE	HIS B:139 , GLU B:205 , HOH B:2117 , HOH B:2118 , HOH B:2119 , HOH B:2172	BINDING SITE FOR RESIDUE MN B1310
3	AC3	SOFTWARE	ILE A:62 , GLY A:63 , GLN A:64 , HIS B:57 , SER B:58 , ILE B:59 , TYR B:69 , GLU B:74 , ASP B:75 , HOH B:2018	BINDING SITE FOR RESIDUE TRS B1311
4	AC4	SOFTWARE	SER A:58 , ILE A:59 , TYR A:69 , LEU A:72 , GLU A:74 , ASP A:75 , ILE B:62 , GLN B:64	BINDING SITE FOR RESIDUE TRS A1311
5	MBS	AUTHOR	HIS A:67 , HIS A:139 , GLU A:205 , ASN A:280	METAL-BINDING SITE

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

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

Asymmetric Unit (13, 26)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_MTSA_STRPN_007 *	I	62	V	MTSA_STRPN	---	---	A/B	I	62	V
02	UniProt	VAR_MTSA_STRPN_008 *	E	81	Q	MTSA_STRPN	---	---	A/B	E	81	Q
03	UniProt	VAR_MTSA_STRPN_009 *	D	83	N	MTSA_STRPN	---	---	A/B	D	83	N
04	UniProt	VAR_MTSA_STRPN_010 *	D	120	E	MTSA_STRPN	---	---	A/B	D	120	E
05	UniProt	VAR_MTSA_STRPN_011 *	Q	130	K	MTSA_STRPN	---	---	A/B	Q	130	K
06	UniProt	VAR_MTSA_STRPN_012 *	I	148	M	MTSA_STRPN	---	---	A/B	I	148	M
07	UniProt	VAR_MTSA_STRPN_013 *	N	164	S	MTSA_STRPN	---	---	A/B	N	164	S
08	UniProt	VAR_MTSA_STRPN_014 *	K	193	N	MTSA_STRPN	---	---	A/B	K	193	N
09	UniProt	VAR_MTSA_STRPN_015 *	A	207	C	MTSA_STRPN	---	---	A/B	A	207	C
10	UniProt	VAR_MTSA_STRPN_016 *	E	234	D	MTSA_STRPN	---	---	A/B	E	234	D
11	UniProt	VAR_MTSA_STRPN_017 *	V	248	T	MTSA_STRPN	---	---	A/B	V	248	T
12	UniProt	VAR_MTSA_STRPN_018 *	Q	285	E	MTSA_STRPN	---	---	A/B	Q	285	E
13	UniProt	VAR_MTSA_STRPN_019 *	S	294	N	MTSA_STRPN	---	---	A/B	S	294	N
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (13, 13)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_MTSA_STRPN_007 *	I	62	V	MTSA_STRPN	---	---	A	I	62	V
02	UniProt	VAR_MTSA_STRPN_008 *	E	81	Q	MTSA_STRPN	---	---	A	E	81	Q
03	UniProt	VAR_MTSA_STRPN_009 *	D	83	N	MTSA_STRPN	---	---	A	D	83	N
04	UniProt	VAR_MTSA_STRPN_010 *	D	120	E	MTSA_STRPN	---	---	A	D	120	E
05	UniProt	VAR_MTSA_STRPN_011 *	Q	130	K	MTSA_STRPN	---	---	A	Q	130	K
06	UniProt	VAR_MTSA_STRPN_012 *	I	148	M	MTSA_STRPN	---	---	A	I	148	M
07	UniProt	VAR_MTSA_STRPN_013 *	N	164	S	MTSA_STRPN	---	---	A	N	164	S
08	UniProt	VAR_MTSA_STRPN_014 *	K	193	N	MTSA_STRPN	---	---	A	K	193	N
09	UniProt	VAR_MTSA_STRPN_015 *	A	207	C	MTSA_STRPN	---	---	A	A	207	C
10	UniProt	VAR_MTSA_STRPN_016 *	E	234	D	MTSA_STRPN	---	---	A	E	234	D
11	UniProt	VAR_MTSA_STRPN_017 *	V	248	T	MTSA_STRPN	---	---	A	V	248	T
12	UniProt	VAR_MTSA_STRPN_018 *	Q	285	E	MTSA_STRPN	---	---	A	Q	285	E
13	UniProt	VAR_MTSA_STRPN_019 *	S	294	N	MTSA_STRPN	---	---	A	S	294	N
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (13, 13)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_MTSA_STRPN_007 *	I	62	V	MTSA_STRPN	---	---	B	I	62	V
02	UniProt	VAR_MTSA_STRPN_008 *	E	81	Q	MTSA_STRPN	---	---	B	E	81	Q
03	UniProt	VAR_MTSA_STRPN_009 *	D	83	N	MTSA_STRPN	---	---	B	D	83	N
04	UniProt	VAR_MTSA_STRPN_010 *	D	120	E	MTSA_STRPN	---	---	B	D	120	E
05	UniProt	VAR_MTSA_STRPN_011 *	Q	130	K	MTSA_STRPN	---	---	B	Q	130	K
06	UniProt	VAR_MTSA_STRPN_012 *	I	148	M	MTSA_STRPN	---	---	B	I	148	M
07	UniProt	VAR_MTSA_STRPN_013 *	N	164	S	MTSA_STRPN	---	---	B	N	164	S
08	UniProt	VAR_MTSA_STRPN_014 *	K	193	N	MTSA_STRPN	---	---	B	K	193	N
09	UniProt	VAR_MTSA_STRPN_015 *	A	207	C	MTSA_STRPN	---	---	B	A	207	C
10	UniProt	VAR_MTSA_STRPN_016 *	E	234	D	MTSA_STRPN	---	---	B	E	234	D
11	UniProt	VAR_MTSA_STRPN_017 *	V	248	T	MTSA_STRPN	---	---	B	V	248	T
12	UniProt	VAR_MTSA_STRPN_018 *	Q	285	E	MTSA_STRPN	---	---	B	Q	285	E
13	UniProt	VAR_MTSA_STRPN_019 *	S	294	N	MTSA_STRPN	---	---	B	S	294	N
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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

(no "Exon" information available for 3ZKA)

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:278
 aligned with MTSA_STRPN | P0A4G2 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:278
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301        
           MTSA_STRPN    32 KLKVVATNSIIADITKNIAGDKIDLHSIVPIGQDPHEYEPLPEDVKKTSEADLIFYNGINLETGGNAWFTKLVENAKKTENKDYFAVSDGVDVIYLEGQNEKGKEDPHAWLNLENGIIFAKNIAKQLSAKDPNNKEFYEKNLKEYTDKLDKLDKESKDKFNKIPAEKKLIVTSEGAFKYFSKAYGVPSAYIWEINTEEEGTPEQIKTLVEKLRQTKVPSLFVESSVDDRPMKTVSQDTNIPIYAQIFTDSIAEQGKEGDSYYSMMKYNLDKIAEGLAK 309
               SCOP domains d3zkaa_ A: automated matches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhh..eeeee.............hhhhhhhhhhh.eeee..........hhhhhhhhhhh......eee.........hhhh........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhh..eeeee........hhhhhhhhhhhhh......eeee....hhhhhhhhhhhh..eeeee.............hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------V------------------Q-N------------------------------------E---------K-----------------M---------------S----------------------------N-------------C--------------------------D-------------T------------------------------------E--------N--------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zka A  32 KLKVVATNSIIADITKNIAGDKIDLHSIVPIGQDPHEYEPLPEDVKKTSEADLIFYNGINLETGGNAWFTKLVENAKKTENKDYFAVSDGVDVIYLEGQNEKGKEDPHAWLNLENGIIFAKNIAKQLSAKDPNNKEFYEKNLKEYTDKLDKLDKESKDKFNKIPAEKKLIVTSEGAFKYFSKAYGVPSAYIWEINTEEEGTPEQIKTLVEKLRQTKVPSLFVESSVDDRPMKTVSQDTNIPIYAQIFTNSIAEQGKEGDSYYSMMKYNLDKIAEGLAK 309
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301

Chain B from PDB  Type:PROTEIN  Length:278
 aligned with MTSA_STRPN | P0A4G2 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:278
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301        
           MTSA_STRPN    32 KLKVVATNSIIADITKNIAGDKIDLHSIVPIGQDPHEYEPLPEDVKKTSEADLIFYNGINLETGGNAWFTKLVENAKKTENKDYFAVSDGVDVIYLEGQNEKGKEDPHAWLNLENGIIFAKNIAKQLSAKDPNNKEFYEKNLKEYTDKLDKLDKESKDKFNKIPAEKKLIVTSEGAFKYFSKAYGVPSAYIWEINTEEEGTPEQIKTLVEKLRQTKVPSLFVESSVDDRPMKTVSQDTNIPIYAQIFTDSIAEQGKEGDSYYSMMKYNLDKIAEGLAK 309
               SCOP domains d3zkab_ B: automated matches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhh..eeeee.............hhhhhhhhhhh.eeee..........hhhhhhhhhh.......eee.........hhhh........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhh..eeeee........hhhhhhhhhhhhh......eeee....hhhhhhhhhhhh..eeeee.............hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------V------------------Q-N------------------------------------E---------K-----------------M---------------S----------------------------N-------------C--------------------------D-------------T------------------------------------E--------N--------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zka B  32 KLKVVATNSIIADITKNIAGDKIDLHSIVPIGQDPHEYEPLPEDVKKTSEADLIFYNGINLETGGNAWFTKLVENAKKTENKDYFAVSDGVDVIYLEGQNEKGKEDPHAWLNLENGIIFAKNIAKQLSAKDPNNKEFYEKNLKEYTDKLDKLDKESKDKFNKIPAEKKLIVTSEGAFKYFSKAYGVPSAYIWEINTEEEGTPEQIKTLVEKLRQTKVPSLFVESSVDDRPMKTVSQDTNIPIYAQIFTNSIAEQGKEGDSYYSMMKYNLDKIAEGLAK 309
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301

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(

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Protein Domains( (-)

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Organisms( (-)

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

Fold: Chelatase-like (149)

Superfamily: Helical backbone metal receptor (102)

Family: TroA-like (17)

Protein domain: automated matches (8)

Pneumococcus (Streptococcus pneumoniae) [TaxId: 1313] (5)

1a	d3zkaa_	A:
1b	d3zkab_	B:

(no "CATH Domain" information available for 3ZKA)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (MTSA_STRPN | P0A4G2)

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: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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3zka)

Biological Units
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	3zka
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UniProtKB/Swiss-Prot
	MTSA_STRPN \| P0A4G2	:	1psz 3zk7 3zk8 3zk9 3ztt 4uto 4utp

3zk7	CRYSTAL STRUCTURE OF PNEUMOCOCCAL SURFACE ANTIGEN PSAA IN THE METAL-FREE, OPEN STATE
3zk8	CRYSTAL STRUCTURE OF PNEUMOCOCCAL SURFACE ANTIGEN PSAA E205Q IN THE METAL-FREE, OPEN STATE
3zk9	CRYSTAL STRUCTURE OF PNEUMOCOCCAL SURFACE ANTIGEN PSAA D280N IN THE METAL-FREE, OPEN STATE
3ztt	CRYSTAL STRUCTURE OF PNEUMOCOCCAL SURFACE ANTIGEN PSAA WITH MANGANESE

Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (13, 26)

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