2E7D - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A NEAT DOMAIN FROM STAPHYLOCOCCUS AUREUS

Authors :   A. Suenaga, Y. Tanaka, M. Yao, I. Kumagai, I. Tanaka, K. Tsumoto

Date :   09 Jan 07 (Deposition) - 22 Jan 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (6x)
Biol. Unit 2: A,B  (3x)

Keywords :   Ig-Like Fold, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Watanabe, Y. Tanaka, A. Suenaga, M. Kuroda, M. Yao, N. Watanabe, F. Arisaka, T. Ohta, I. Tanaka, K. Tsumoto
Structural Basis For Multimeric Heme Complexation Through A Specific Protein-Heme Interaction: The Case Of The Third Neat Domain Of Isdh From Staphylococcus Aureus
J. Biol. Chem. V. 283 28649 2008
PubMed-ID: 18667422 | Reference-DOI: 10.1074/JBC.M803383200

Molecule 1 - HYPOTHETICAL PROTEIN ISDH
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDBHT3
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	NEAT DOMAIN, RESIDUE 539-664
	Gene	:	ISDH
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Strain	:	MU50
	Synonym	:	HEME BINDING PROTEIN

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (6x)	:	A	B
Biological Unit 2 (3x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 36)

No.	Name	Count	Type	Full Name
1	ACT	6	Ligand/Ion	ACETATE ION
2	GOL	12	Ligand/Ion	GLYCEROL
3	SO4	18	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 18)

No.	Name	Count	Type	Full Name
1	ACT	3	Ligand/Ion	ACETATE ION
2	GOL	6	Ligand/Ion	GLYCEROL
3	SO4	9	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:37 , HIS A:38 , LYS A:56 , LYS A:79 , HOH A:5625 , HOH A:5643	BINDING SITE FOR RESIDUE SO4 A 5610
2	AC2	SOFTWARE	THR A:12 , ASP A:13 , LEU A:14 , LYS A:76 , ASN A:106 , HOH A:5651	BINDING SITE FOR RESIDUE SO4 A 5612
3	AC3	SOFTWARE	LYS A:93 , ALA A:94 , VAL A:95	BINDING SITE FOR RESIDUE ACT A 1019
4	AC4	SOFTWARE	ASP A:58 , TRP A:61 , LYS A:62 , ASP A:63 , LEU A:64 , ARG A:83	BINDING SITE FOR RESIDUE GOL A 3147
5	AC5	SOFTWARE	VAL B:36 , GLU B:37 , HIS B:38 , LYS B:56 , HOH B:5631	BINDING SITE FOR RESIDUE SO4 B 5611
6	AC6	SOFTWARE	ASP B:58 , TRP B:61 , LYS B:62 , ASP B:63 , LEU B:64 , ARG B:83	BINDING SITE FOR RESIDUE GOL B 3148

(no "SS Bond" information available for 2E7D)

Asymmetric Unit

No.	Residues
1	His A:38	-	Pro A:39
2	His B:38	-	Pro B:39

(no "SAP(SNP)/Variant" information available for 2E7D)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NEAT	PS50978	NEAT domain profile.	ISDH_STAAM	105-232 345-471 543-660	1	- - A:10-124

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NEAT	PS50978	NEAT domain profile.	ISDH_STAAM	105-232 345-471 543-660	6	- - A:10-124

Biological Unit 2 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NEAT	PS50978	NEAT domain profile.	ISDH_STAAM	105-232 345-471 543-660	3	- - A:10-124

(no "Exon" information available for 2E7D)

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:116
 aligned with ISDH_STAAM | Q931P4 from UniProtKB/Swiss-Prot  Length:891

    Alignment length:116
                                   551       561       571       581       591       601       611       621       631       641       651      
           ISDH_STAAM   542 DQLTDLQEAHFVVFESEENSESVMDGFVEHPFYTATLNGQKYVVMKTKDDSYWKDLIVEGKRVTTVSKDPKNNSRTLIFPYIPDKAVYNAIVKVVVANIGYEGQYHVRIINQDINT 657
               SCOP domains d2e7da_ A: automated matches                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.eeeee......hhhhhhh...eeeeee..eeeeeee..hhh.eeeeee..ee.eeeeee....eeeeeee......eeeeeeeeeehhh.eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -NEAT  PDB: A:10-124 UniProt: 543-660                                                                                PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 2e7d A   9 DQLTDLQEAHFVVFESEENSESVMDGFVEHPFYTATLNGQKYVVMKTKDDSYWKDLIVEGKRVTTVSKDPKNNSRTLIFPYIPDKAVYNAIVKVVVANIGYEGQYHVRIINQDINT 124
                                    18        28        38        48        58        68        78        88        98       108       118

Chain B from PDB  Type:PROTEIN  Length:112
 aligned with ISDH_STAAM | Q931P4 from UniProtKB/Swiss-Prot  Length:891

    Alignment length:112
                                   553       563       573       583       593       603       613       623       633       643       653  
           ISDH_STAAM   544 LTDLQEAHFVVFESEENSESVMDGFVEHPFYTATLNGQKYVVMKTKDDSYWKDLIVEGKRVTTVSKDPKNNSRTLIFPYIPDKAVYNAIVKVVVANIGYEGQYHVRIINQDI 655
               SCOP domains d2e7db_ B: automated matches                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeee......hhhhhhh....eeeee..eeeeeee..hhh.eeeeee..ee.eeeeeehhhheeeeeee......eeeeeeeeeehhh.eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE NEAT  PDB: - UniProt: 543-660                                                                                    PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 2e7d B  11 LTDLQEAHFVVFESEENSESVMDGFVEHPFYTATLNGQKYVVMKTKDDSYWKDLIVEGKRVTTVSKDPKNNSRTLIFPYIPDKAVYNAIVKVVVANIGYEGQYHVRIINQDI 122
                                    20        30        40        50        60        70        80        90       100       110       120

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 beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: NEAT domain-like (27)

Family: automated matches (13)

Protein domain: automated matches (13)

Staphylococcus aureus [TaxId: 158879] (7)

1a	d2e7da_	A:
1b	d2e7db_	B:

(no "CATH Domain" information available for 2E7D)

(no "Pfam Domain" information available for 2E7D)

Asymmetric Unit(hide GO term definitions)

Chain A,B (ISDH_STAAM | Q931P4)


GO:0005618	cell wall	The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric Unit
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	Cis Peptide Bonds
		His A:38 - Pro A:39	[ RasMol ]
		His B:38 - Pro B:39	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	2e7d
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		Domain Information	:	XDom
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	ISDH_STAAM \| Q931P4
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UniProtKB/Swiss-Prot
	ISDH_STAAM \| Q931P4	:	2z6f 3qug 3quh 3vtm 3vua

2h3k	THE OTHER NEAT DOMAIN OF ISDH
2ite	NEAT DOMAIN OF ISDA
2itf	NEAT DOMAIN OF ISDA COMPLEXED WITH HEMIN
2o1a	NEAT DOMAIN OF ISDA WHICH IS A HOMOLOGUE PROTEIN OF ISDH

Description

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Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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