3RUR - 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)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Biological Unit 6 (Jmol Viewer)

Title :   STAPHYLOCOCCUS AUREUS HEME-BOUND SELENOMETHIONINE-LABELED ISDB-N2

Authors :   C. F. M. Gaudin, J. C. Grigg, A. L. Arrieta, M. E. P. Murphy

Date :   05 May 11 (Deposition) - 18 May 11 (Release) - 29 Jun 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: A,D  (1x)
Biol. Unit 6: B,C  (1x)

Keywords :   Heme Protein, Heme Uptake, Neat Domain, Heme Binding, Cell Wall, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. F. Gaudin, J. C. Grigg, A. L. Arrieta, M. E. Murphy
Unique Heme-Iron Coordination By The Hemoglobin Receptor Isdb Of Staphylococcus Aureus.
Biochemistry V. 50 5443 2011
PubMed-ID: 21574663 | Reference-DOI: 10.1021/BI200369P

Molecule 1 - IRON-REGULATED SURFACE DETERMINANT PROTEIN B
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	NEAT DOMAIN (UNP RESIDUES 341-459)
	Gene	:	FRPB, ISDB, SA0976, SASJ, SIRH
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
	Organism Taxid	:	158879
	Strain	:	N315
	Synonym	:	FUR-REGULATED PROTEIN B, STAPHYLOCOCCAL IRON-REGULATED PROTEIN H, STAPHYLOCOCCUS AUREUS SURFACE PROTEIN J

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D
Biological Unit 5 (1x)	:	A			D
Biological Unit 6 (1x)	:		B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 37)

No.	Name	Count	Type	Full Name
1	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	MG	5	Ligand/Ion	MAGNESIUM ION
3	MSE	28	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	7	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 8)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	7	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (2, 8)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	7	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 4 (2, 8)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	7	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 5 (2, 16)

No.	Name	Count	Type	Full Name
1	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	14	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 6 (2, 16)

No.	Name	Count	Type	Full Name
1	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	14	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:7 , HOH A:92 , GLU A:354 , SER A:361 , MSE A:362 , PHE A:366 , TRP A:392 , VAL A:433 , VAL A:435 , ILE A:438 , TYR A:440 , TYR A:444 , VAL A:446 , HEM D:200 , THR D:365 , TYR D:391 , ILE D:438	BINDING SITE FOR RESIDUE HEM A 200
2	AC2	SOFTWARE	HOH A:151 , HOH A:185 , GLU A:354 , HOH A:526 , HOH D:180 , HOH D:489	BINDING SITE FOR RESIDUE MG A 495
3	AC3	SOFTWARE	HOH A:56 , LYS A:432 , HOH B:1 , HOH B:226 , GLU B:354 , SER B:361 , MSE B:362 , MSE B:363 , PHE B:366 , TYR B:391 , TRP B:392 , VAL B:433 , ILE B:438 , TYR B:440 , TYR B:444 , VAL B:446 , HOH B:461 , HOH B:508 , THR C:365	BINDING SITE FOR RESIDUE HEM B 200
4	AC4	SOFTWARE	GLU B:354 , HOH B:469 , HOH B:528 , HOH C:57 , HOH C:75 , HOH C:461	BINDING SITE FOR RESIDUE MG B 225
5	AC5	SOFTWARE	THR B:365 , ASN B:388 , HOH C:6 , HOH C:55 , GLU C:354 , SER C:361 , MSE C:362 , PHE C:366 , TYR C:391 , TRP C:392 , VAL C:433 , ILE C:438 , TYR C:440 , TYR C:444 , VAL C:446 , HOH C:474	BINDING SITE FOR RESIDUE HEM C 200
6	AC6	SOFTWARE	HOH B:99 , HOH B:524 , HOH C:96 , HOH C:98 , GLU C:354 , HOH C:504	BINDING SITE FOR RESIDUE MG C 95
7	AC7	SOFTWARE	HOH C:91 , HOH C:155 , ASP C:428 , HOH C:525 , ASP D:428 , HOH D:499	BINDING SITE FOR RESIDUE MG C 166
8	AC8	SOFTWARE	HEM A:200 , HOH A:336 , THR A:365 , PHE A:366 , ASN A:388 , HOH D:4 , HOH D:54 , HOH D:214 , GLU D:354 , SER D:361 , MSE D:362 , PHE D:366 , TYR D:391 , TRP D:392 , VAL D:433 , ILE D:438 , TYR D:440 , TYR D:444 , VAL D:446 , HOH D:472	BINDING SITE FOR RESIDUE HEM D 200
9	AC9	SOFTWARE	HOH A:485 , HOH A:527 , HOH D:54 , HOH D:184 , GLU D:354 , HOH D:498	BINDING SITE FOR RESIDUE MG D 460

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

Asymmetric Unit

No.	Residues
1	His A:369	-	Pro A:370
2	His B:369	-	Pro B:370
3	His C:369	-	Pro C:370
4	His D:369	-	Pro D:370

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NEAT	PS50978	NEAT domain profile.	ISDB_STAAN	144-269 341-458	4	- A:341-455 B:341-455 C:341-456 D:341-454

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NEAT	PS50978	NEAT domain profile.	ISDB_STAAN	144-269 341-458	1	- A:341-455 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NEAT	PS50978	NEAT domain profile.	ISDB_STAAN	144-269 341-458	1	- - B:341-455 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NEAT	PS50978	NEAT domain profile.	ISDB_STAAN	144-269 341-458	1	- - - C:341-456 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NEAT	PS50978	NEAT domain profile.	ISDB_STAAN	144-269 341-458	1	- - - - D:341-454

Biological Unit 5 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NEAT	PS50978	NEAT domain profile.	ISDB_STAAN	144-269 341-458	2	- A:341-455 - - D:341-454

Biological Unit 6 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NEAT	PS50978	NEAT domain profile.	ISDB_STAAN	144-269 341-458	2	- - B:341-455 C:341-456 -

(no "Exon" information available for 3RUR)

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:115
 aligned with ISDB_STAAN | Q7A656 from UniProtKB/Swiss-Prot  Length:645

    Alignment length:115
                                   350       360       370       380       390       400       410       420       430       440       450     
           ISDB_STAAN   341 KMTDLQDTKYVVYESVENNESMMDTFVKHPIKTGMLNGKKYMVMETTNDDYWKDFMVEGQRVRTISKDAKNNTRTIIFPYVEGKTLYDAIVKVHVKTIDYDGQYHVRIVDKEAFT 455
               SCOP domains d3rura_ A: automated matches                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee..eeeee......hhhhhhh....eeeee..eeeeeeee.hhh.eeeeee..ee.eeeeee....eeeeeee......eeeeeeeeeehhhheeeeeeeeeee.hhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE NEAT  PDB: A:341-455 UniProt: 341-458                                                                               PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 3rur A 341 KmTDLQDTKYVVYESVENNESmmDTFVKHPIKTGmLNGKKYmVmETTNDDYWKDFmVEGQRVRTISKDAKNNTRTIIFPYVEGKTLYDAIVKVHVKTIDYDGQYHVRIVDKEAFT 455
                             |     350       360 ||    370    |  380 | |   390     | 400       410       420       430       440       450     
                             |                 362-MSE      375-MSE  | |         396-MSE                                                       
                           342-MSE              363-MSE            382-MSE                                                                     
                                                                     384-MSE

Chain B from PDB  Type:PROTEIN  Length:117
 aligned with ISDB_STAAN | Q7A656 from UniProtKB/Swiss-Prot  Length:645

    Alignment length:117
                                   348       358       368       378       388       398       408       418       428       438       448       
           ISDB_STAAN   339 NEKMTDLQDTKYVVYESVENNESMMDTFVKHPIKTGMLNGKKYMVMETTNDDYWKDFMVEGQRVRTISKDAKNNTRTIIFPYVEGKTLYDAIVKVHVKTIDYDGQYHVRIVDKEAFT 455
               SCOP domains d3rurb_ B: automated matches                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..eeeee......hhhhhhh....eeeee..eeeeeeee.hhh.eeeeee..ee.eeeeee....eeeeeee......eeeeeeeeeehhhheeeeeeeeeee.hhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --NEAT  PDB: B:341-455 UniProt: 341-458                                                                               PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3rur B 339 GSKmTDLQDTKYVVYESVENNESmmDTFVKHPIKTGmLNGKKYmVmETTNDDYWKDFmVEGQRVRTISKDAKNNTRTIIFPYVEGKTLYDAIVKVHVKTIDYDGQYHVRIVDKEAFT 455
                               |   348       358   ||  368      |378   | | 388       398       408       418       428       438       448       
                             342-MSE             362-MSE      375-MSE  | |         396-MSE                                                       
                                                  363-MSE            382-MSE                                                                     
                                                                       384-MSE

Chain C from PDB  Type:PROTEIN  Length:117
 aligned with ISDB_STAAN | Q7A656 from UniProtKB/Swiss-Prot  Length:645

    Alignment length:117
                                   349       359       369       379       389       399       409       419       429       439       449       
           ISDB_STAAN   340 EKMTDLQDTKYVVYESVENNESMMDTFVKHPIKTGMLNGKKYMVMETTNDDYWKDFMVEGQRVRTISKDAKNNTRTIIFPYVEGKTLYDAIVKVHVKTIDYDGQYHVRIVDKEAFTK 456
               SCOP domains d3rurc_ C: automated matches                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..eeeee......hhhhhhh....eeeee..eeeeeeee.hhh.eeeeee..ee.eeeeee....eeeeeee......eeeeeeeeeehhhheeeeeeeeeeehhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -NEAT  PDB: C:341-456 UniProt: 341-458                                                                                PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3rur C 340 SKmTDLQDTKYVVYESVENNESmmDTFVKHPIKTGmLNGKKYmVmETTNDDYWKDFmVEGQRVRTISKDAKNNTRTIIFPYVEGKTLYDAIVKVHVKTIDYDGQYHVRIVDKEAFTK 456
                              |    349       359  ||   369     | 379  | |  389      |399       409       419       429       439       449       
                            342-MSE             362-MSE      375-MSE  | |         396-MSE                                                        
                                                 363-MSE            382-MSE                                                                      
                                                                      384-MSE

Chain D from PDB  Type:PROTEIN  Length:115
 aligned with ISDB_STAAN | Q7A656 from UniProtKB/Swiss-Prot  Length:645

    Alignment length:115
                                   349       359       369       379       389       399       409       419       429       439       449     
           ISDB_STAAN   340 EKMTDLQDTKYVVYESVENNESMMDTFVKHPIKTGMLNGKKYMVMETTNDDYWKDFMVEGQRVRTISKDAKNNTRTIIFPYVEGKTLYDAIVKVHVKTIDYDGQYHVRIVDKEAF 454
               SCOP domains d3rurd_ D: automated matches                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -NEAT-3rurD01 D:341-454                                                                                             Pfam domains (1)
           Pfam domains (2) -NEAT-3rurD02 D:341-454                                                                                             Pfam domains (2)
           Pfam domains (3) -NEAT-3rurD03 D:341-454                                                                                             Pfam domains (3)
           Pfam domains (4) -NEAT-3rurD04 D:341-454                                                                                             Pfam domains (4)
         Sec.struct. author ...eeeee..eeeee......hhhhhhh....eeeee..eeeeeeee.hhh.eeeeee..ee.eeeeee....eeeeeee......eeeeeeeeeehhhheeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -NEAT  PDB: D:341-454 UniProt: 341-458                                                                              PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 3rur D 340 SKmTDLQDTKYVVYESVENNESmmDTFVKHPIKTGmLNGKKYmVmETTNDDYWKDFmVEGQRVRTISKDAKNNTRTIIFPYVEGKTLYDAIVKVHVKTIDYDGQYHVRIVDKEAF 454
                              |    349       359  ||   369     | 379  | |  389      |399       409       419       429       439       449     
                            342-MSE             362-MSE      375-MSE  | |         396-MSE                                                      
                                                 363-MSE            382-MSE                                                                    
                                                                      384-MSE

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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(

)

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	d3rura_	A:
1b	d3rurb_	B:
1c	d3rurc_	C:
1d	d3rurd_	D:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: NEAT (8)

Staphylococcus aureus (strain N315) (3)

1a	NEAT-3rurD01	D:341-454
1b	NEAT-3rurD02	D:341-454
1c	NEAT-3rurD03	D:341-454
1d	NEAT-3rurD04	D:341-454

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (ISDB_STAAN | Q7A656)

molecular function
	GO:0015232	heme transporter activity	Enables 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.
	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.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
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: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:369 - Pro A:370	[ RasMol ]
		His B:369 - Pro B:370	[ RasMol ]
		His C:369 - Pro C:370	[ RasMol ]
		His D:369 - Pro D:370	[ RasMol ]

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	3rur
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(no "Related Entries Specified in the PDB File" available for 3RUR)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 37)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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