2O6P - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE HEME-ISDC COMPLEX

Authors :   K. H. Sharp, S. Schneider, A. Cockayne, M. Paoli

Date :   08 Dec 06 (Deposition) - 06 Feb 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)
Biol. Unit 4: A (1x),B (1x)
Biol. Unit 5: A (1x),B (1x)

Keywords :   Beta Barrel, Protein-Heme Complex, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. H. Sharp, S. Schneider, A. Cockayne, M. Paoli
Crystal Structure Of The Heme-Isdc Complex, The Central Conduit Of The Isd Iron/Heme Uptake System In Staphylococcu Aureus
To Be Published
PubMed: search

Molecule 1 - IRON-REGULATED SURFACE DETERMINANT PROTEIN C
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PGAT2
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 28-188
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
	Organism Taxid	:	158879
	Strain	:	N315
	Synonym	:	ISDC, STAPHYLOCOCCAL IRON-REGULATED PROTEIN D

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A	B
Biological Unit 4 (1x)	:	A (1x)	B (1x)
Biological Unit 5 (1x)	:	A (1x)	B (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	ZN	6	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 5 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:42 , ASP A:114 , ASP B:133 , HIS B:135	BINDING SITE FOR RESIDUE ZN B 1001
02	AC2	SOFTWARE	HEM A:190 , HIS B:134 , HOH B:1051 , HOH B:1103	BINDING SITE FOR RESIDUE ZN B 1003
03	AC3	SOFTWARE	GLY A:28 , HIS A:76 , GLU A:123 , GLY B:28	BINDING SITE FOR RESIDUE ZN B 1002
04	AC4	SOFTWARE	HIS A:134 , HOH A:1053 , HOH A:1065 , HEM B:190	BINDING SITE FOR RESIDUE ZN A 1004
05	AC5	SOFTWARE	HIS A:74 , LYS B:58 , HOH B:1088 , HOH B:1098	BINDING SITE FOR RESIDUE ZN B 1005
06	AC6	SOFTWARE	ASP A:133 , HIS A:135 , HOH A:1083	BINDING SITE FOR RESIDUE ZN A 1006
07	AC7	SOFTWARE	SER A:82 , GLU A:84 , GLY A:85 , LYS A:116	BINDING SITE FOR RESIDUE CL A 1007
08	AC8	SOFTWARE	SER B:82 , GLU B:84 , GLY B:85 , HOH B:1089 , HOH B:1100	BINDING SITE FOR RESIDUE CL B 1008
09	AC9	SOFTWARE	LYS A:40 , SER A:47 , ILE A:48 , TYR A:52 , VAL A:119 , PHE A:130 , TYR A:132 , TYR A:136 , ILE A:138 , HOH A:1013 , HOH A:1044 , HOH A:1059 , PHE B:130 , LYS B:131 , TYR B:132 , HIS B:134 , HEM B:190 , ZN B:1003	BINDING SITE FOR RESIDUE HEM A 190
10	BC1	SOFTWARE	TYR A:132 , HIS A:134 , TYR A:136 , HEM A:190 , ZN A:1004 , HOH A:1053 , LYS B:40 , SER B:47 , ILE B:48 , TYR B:52 , ILE B:78 , ILE B:117 , VAL B:119 , TYR B:132 , TYR B:136 , ILE B:138 , HOH B:1014 , HOH B:1032	BINDING SITE FOR RESIDUE HEM B 190

(no "SS Bond" information available for 2O6P)

Asymmetric Unit

No.	Residues
1	Lys A:55	-	Pro A:56
2	Lys B:55	-	Pro B:56
3	Glu B:123	-	Lys B:124

(no "SAP(SNP)/Variant" information available for 2O6P)

(no "PROSITE Motif" information available for 2O6P)

(no "Exon" information available for 2O6P)

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:123
 aligned with ISDC_STAA8 | Q8KQR1 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:123
                                    37        47        57        67        77        87        97       107       117       127       137       147   
           ISDC_STAA8    28 AADSGTLNYEVYKYNTNDTSIANDYFNKPAKYIKKNGKLYVQITVNHSHWITGMSIEGHKENIISKNTAKDERTSEFEVSKLNGKIDGKIDVYIDEKVNGKPFKYDHHYNITYKFNGPTDVAG 150
               SCOP domains -d2o6pa1 A:29-150 Iron-regulated surface determinant protein C, IsdC                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee......hhhhhhh...eeeeee..eeeeeeeee....eeeeee..ee.eeeeee....eeeeeeee...eeeeeeeeeeeeeeee..eeeeeeeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o6p A  28 GSDSGTLNYEVYKYNTNDTSIANDYFNKPAKYIKKNGKLYVQITVNHSHWITGMSIEGHKENIISKNTAKDERTSEFEVSKLNGKIDGKIDVYIDEKVNGKPFKYDHHYNITYKFNGPTDVAG 150
                                    37        47        57        67        77        87        97       107       117       127       137       147

Chain A from PDB  Type:PROTEIN  Length:123
 aligned with ISDC_STAAN | Q7A654 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:123
                                    37        47        57        67        77        87        97       107       117       127       137       147   
           ISDC_STAAN    28 AADSGTLNYEVYKYNTNDTSIANDYFNKPAKYIKKNGKLYVQITVNHSHWITGMSIEGHKENIISKNTAKDERTSEFEVSKLNGKIDGKIDVYIDEKVNGKPFKYDHHYNITYKFNGPTDVAG 150
               SCOP domains -d2o6pa1 A:29-150 Iron-regulated surface determinant protein C, IsdC                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee......hhhhhhh...eeeeee..eeeeeeeee....eeeeee..ee.eeeeee....eeeeeeee...eeeeeeeeeeeeeeee..eeeeeeeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o6p A  28 GSDSGTLNYEVYKYNTNDTSIANDYFNKPAKYIKKNGKLYVQITVNHSHWITGMSIEGHKENIISKNTAKDERTSEFEVSKLNGKIDGKIDVYIDEKVNGKPFKYDHHYNITYKFNGPTDVAG 150
                                    37        47        57        67        77        87        97       107       117       127       137       147

Chain B from PDB  Type:PROTEIN  Length:119
 aligned with ISDC_STAA8 | Q8KQR1 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:119
                                    37        47        57        67        77        87        97       107       117       127       137         
           ISDC_STAA8    28 AADSGTLNYEVYKYNTNDTSIANDYFNKPAKYIKKNGKLYVQITVNHSHWITGMSIEGHKENIISKNTAKDERTSEFEVSKLNGKIDGKIDVYIDEKVNGKPFKYDHHYNITYKFNGPT 146
               SCOP domains d2o6pb_ B: Iron-regulated surface determinant protein C, IsdC                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --NEAT-2o6pB01 B:30-146                                                                                                 Pfam domains (1)
           Pfam domains (2) --NEAT-2o6pB02 B:30-146                                                                                                 Pfam domains (2)
         Sec.struct. author ..eeeee.eeeee......hhhhhhh...eeeeee..eeeeeeeee....eeeeee..ee.eeeeee....eeeeeeee...eeeeeeeeeeeeee......eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 2o6p B  28 GSDSGTLNYEVYKYNTNDTSIANDYFNKPAKYIKKNGKLYVQITVNHSHWITGMSIEGHKENIISKNTAKDERTSEFEVSKLNGKIDGKIDVYIDEKVNGKPFKYDHHYNITYKFNGPT 146
                                    37        47        57        67        77        87        97       107       117       127       137

Chain B from PDB  Type:PROTEIN  Length:119
 aligned with ISDC_STAAN | Q7A654 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:119
                                    37        47        57        67        77        87        97       107       117       127       137         
           ISDC_STAAN    28 AADSGTLNYEVYKYNTNDTSIANDYFNKPAKYIKKNGKLYVQITVNHSHWITGMSIEGHKENIISKNTAKDERTSEFEVSKLNGKIDGKIDVYIDEKVNGKPFKYDHHYNITYKFNGPT 146
               SCOP domains d2o6pb_ B: Iron-regulated surface determinant protein C, IsdC                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --NEAT-2o6pB01 B:30-146                                                                                                 Pfam domains (1)
           Pfam domains (2) --NEAT-2o6pB02 B:30-146                                                                                                 Pfam domains (2)
         Sec.struct. author ..eeeee.eeeee......hhhhhhh...eeeeee..eeeeeeeee....eeeeee..ee.eeeeee....eeeeeeee...eeeeeeeeeeeeee......eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 2o6p B  28 GSDSGTLNYEVYKYNTNDTSIANDYFNKPAKYIKKNGKLYVQITVNHSHWITGMSIEGHKENIISKNTAKDERTSEFEVSKLNGKIDGKIDVYIDEKVNGKPFKYDHHYNITYKFNGPT 146
                                    37        47        57        67        77        87        97       107       117       127       137

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	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: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: NEAT domain-like (27)

Family: NEAT domain (14)

Protein domain: Iron-regulated surface determinant protein C, IsdC (1)

Staphylococcus aureus [TaxId: 1280] (1)

1a	d2o6pa1	A:29-150
1b	d2o6pb_	B:

(no "CATH Domain" information available for 2O6P)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: NEAT] (8)

Family: NEAT (8)

Staphylococcus aureus (strain N315) (3)

1a	NEAT-2o6pB01	B:30-146
1b	NEAT-2o6pB02	B:30-146

Asymmetric Unit(hide GO term definitions)

Chain A,B (ISDC_STAAN | Q7A654)

molecular function
	GO:0030492	hemoglobin binding	Interacting selectively and non-covalently with hemoglobin, an oxygen carrying, conjugated protein containing four heme groups and globin.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0015886	heme transport	The directed movement of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
	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:0009274	peptidoglycan-based cell wall	A protective structure outside the cytoplasmic membrane composed of peptidoglycan (also known as murein), a molecule made up of a glycan (sugar) backbone of repetitively alternating N-acetylglucosamine and N-acetylmuramic acid with short, attached, cross-linked peptide chains containing unusual amino acids. An example of this component is found in Escherichia coli.

Chain A,B (ISDC_STAA8 | Q8KQR1)

molecular function
	GO:0030492	hemoglobin binding	Interacting selectively and non-covalently with hemoglobin, an oxygen carrying, conjugated protein containing four heme groups and globin.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0015886	heme transport	The directed movement of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
	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:0009274	peptidoglycan-based cell wall	A protective structure outside the cytoplasmic membrane composed of peptidoglycan (also known as murein), a molecule made up of a glycan (sugar) backbone of repetitively alternating N-acetylglucosamine and N-acetylmuramic acid with short, attached, cross-linked peptide chains containing unusual amino acids. An example of this component is found in Escherichia coli.

Asymmetric Unit
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	Cis Peptide Bonds
		Glu B:123 - Lys B:124	[ RasMol ]
		Lys A:55 - Pro A:56	[ RasMol ]
		Lys B:55 - Pro B:56	[ RasMol ]

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