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Title :   CRYSTAL STRUCTURE OF DPS FROM STAPHYLOCOCCUS AUREUS

Authors :   Y. Tanaka, M. Yao, N. Watanabe, I. Tanaka

Date :   02 Nov 05 (Deposition) - 17 Oct 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Four Helix Bundle, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Tanaka, M. Yao, N. Watanabe, I. Tanaka
Crystal Structure Of Dps From Staphylococcus Aureus
To Be Published
PubMed: search

Molecule 1 - DPS FAMILY PROTEIN
	Chains	:	A, B, C, D
	EC Number	:	4.2.1.52
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
	Organism Taxid	:	93062
	Strain	:	COL
	Synonym	:	DPS

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (3x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:25 , LYS A:84 , ASP A:102 , ASN A:105 , LEU A:147 , HOH A:2674 , HOH A:2676	BINDING SITE FOR RESIDUE GOL A 2647
2	AC2	SOFTWARE	ASP A:127 , HOH A:2781 , ASP B:127 , ASP C:127	BINDING SITE FOR RESIDUE GOL B 3647

(no "SS Bond" information available for 2D5K)

(no "Cis Peptide Bond" information available for 2D5K)

(no "SAP(SNP)/Variant" information available for 2D5K)

(no "PROSITE Motif" information available for 2D5K)

(no "Exon" information available for 2D5K)

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:148
 aligned with A0A0H2X069_S | A0A0H2X069 from UniProtKB/TrEMBL  Length:147

    Alignment length:148
                                                                                                                                                                           147  
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141     |  
         A0A0H2X069_S     2 SNQQDVVKELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHVKFEELYNEASQYVDELAERILAVGGNPVGTLTECLEQSIVKEAAKGYSAEQMVEELSQDFTNISKQLENAIEIAGNAGDDVSEDMFIGMQTSVDKHNWMFKSYLS--   -
               SCOP domains d2d5ka_ A: automated matches                                                                                                                         SCOP domains
               CATH domains 2d5kA00 A:3-150  [code=1.20.1260.10, no name defined]                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d5k A   3 SNQQDVVKELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHVKFEELYNEASQYVDELAERILAVGGNPVGTLTECLEQSIVKEAAKGYSAEQMVEELSQDFTNISKQLENAIEIAGNAGDDVSEDMFIGMQTSVDKHNWMFKSYLSLE 150
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142

Chain B from PDB  Type:PROTEIN  Length:149
 aligned with A0A0H2X069_S | A0A0H2X069 from UniProtKB/TrEMBL  Length:147

    Alignment length:149
                                                                                                                                                                            147  
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      |  
         A0A0H2X069_S     1 MSNQQDVVKELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHVKFEELYNEASQYVDELAERILAVGGNPVGTLTECLEQSIVKEAAKGYSAEQMVEELSQDFTNISKQLENAIEIAGNAGDDVSEDMFIGMQTSVDKHNWMFKSYLS--   -
               SCOP domains d2d5kb_ B: automated matches                                                                                                                          SCOP domains
               CATH domains 2d5kB00 B:2-150  [code=1.20.1260.10, no name defined]                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d5k B   2 ASNQQDVVKELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHVKFEELYNEASQYVDELAERILAVGGNPVGTLTECLEQSIVKEAAKGYSAEQMVEELSQDFTNISKQLENAIEIAGNAGDDVSEDMFIGMQTSVDKHNWMFKSYLSLE 150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain C from PDB  Type:PROTEIN  Length:147
 aligned with A0A0H2X069_S | A0A0H2X069 from UniProtKB/TrEMBL  Length:147

    Alignment length:147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       
         A0A0H2X069_S     1 MSNQQDVVKELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHVKFEELYNEASQYVDELAERILAVGGNPVGTLTECLEQSIVKEAAKGYSAEQMVEELSQDFTNISKQLENAIEIAGNAGDDVSEDMFIGMQTSVDKHNWMFKSYLS 147
               SCOP domains d2d5kc_ C: automated matches                                                                                                                        SCOP domains
               CATH domains 2d5kC00 C:2-148  [code=1.20.1260.10, no name defined]                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d5k C   2 ASNQQDVVKELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHVKFEELYNEASQYVDELAERILAVGGNPVGTLTECLEQSIVKEAAKGYSAEQMVEELSQDFTNISKQLENAIEIAGNAGDDVSEDMFIGMQTSVDKHNWMFKSYLS 148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain D from PDB  Type:PROTEIN  Length:147
 aligned with A0A0H2X069_S | A0A0H2X069 from UniProtKB/TrEMBL  Length:147

    Alignment length:147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       
         A0A0H2X069_S     1 MSNQQDVVKELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHVKFEELYNEASQYVDELAERILAVGGNPVGTLTECLEQSIVKEAAKGYSAEQMVEELSQDFTNISKQLENAIEIAGNAGDDVSEDMFIGMQTSVDKHNWMFKSYLS 147
               SCOP domains d2d5kd_ D: automated matches                                                                                                                        SCOP domains
               CATH domains 2d5kD00 D:2-148  [code=1.20.1260.10, no name defined]                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d5k D   2 ASNQQDVVKELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHVKFEELYNEASQYVDELAERILAVGGNPVGTLTECLEQSIVKEAAKGYSAEQMVEELSQDFTNISKQLENAIEIAGNAGDDVSEDMFIGMQTSVDKHNWMFKSYLS 148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

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(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Ferritin-like (533)

Superfamily: Ferritin-like (489)

Family: automated matches (54)

Protein domain: automated matches (54)

Staphylococcus aureus [TaxId: 93062] (1)

1a	d2d5ka_	A:
1b	d2d5kb_	B:
1c	d2d5kc_	C:
1d	d2d5kd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Ferritin; (180)

Homologous Superfamily: [code=1.20.1260.10, no name defined] (180)

Aureus col (Staphylococcus aureus subsp) (1)

1a	2d5kB00	B:2-150
1b	2d5kA00	A:3-150
1c	2d5kC00	C:2-148
1d	2d5kD00	D:2-148

(no "Pfam Domain" information available for 2D5K)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 2D5K)

Asymmetric Unit
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Biological Unit
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1dps	CRYSTAL STRUCTURE OF A HOMOLOGOUS PROTEIN
1ji5	CRYSTAL STRUCTURE OF A HOMOLOGOUS PROTEIN
1jig	CRYSTAL STRUCTURE OF A HOMOLOGOUS PROTEIN
1n1q	CRYSTAL STRUCTURE OF A HOMOLOGOUS PROTEIN
1qgh	CRYSTAL STRUCTURE OF A HOMOLOGOUS PROTEIN
1umn	CRYSTAL STRUCTURE OF A HOMOLOGOUS PROTEIN

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