3QZM - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   STAPHYLOCOCCUS AUREUS ISDA NEAT DOMAIN H83A VARIANT IN COMPLEX WITH HEME

Authors :   J. C. Grigg, C. X. Mao, M. E. P. Murphy

Date :   06 Mar 11 (Deposition) - 31 Aug 11 (Release) - 02 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.25

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

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

Reference :   J. C. Grigg, C. X. Mao, M. E. Murphy
Iron-Coordinating Tyrosine Is A Key Determinant Of Neat Domain Heme Transfer.
J. Mol. Biol. V. 413 684 2011
PubMed-ID: 21893067 | Reference-DOI: 10.1016/J.JMB.2011.08.047

Molecule 1 - IRON-REGULATED SURFACE DETERMINANT PROTEIN A
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 62-184
	Gene	:	FRPA, ISDA, SA0977, STBA
	Mutation	:	YES
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
	Organism Taxid	:	158879
	Strain	:	N315
	Synonym	:	FUR-REGULATED PROTEIN A, STAPHYLOCOCCAL TRANSFERRIN-BINDING PROTEIN 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 (3, 15)

No.	Name	Count	Type	Full Name
1	GOL	11	Ligand/Ion	GLYCEROL
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	GOL	5	Ligand/Ion	GLYCEROL
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 7)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GOL A:12 , HOH A:47 , LYS A:75 , SER A:82 , ALA A:83 , MET A:84 , TYR A:87 , TRP A:113 , ILE A:159 , ILE A:164 , TYR A:166 , TYR A:170 , THR A:172 , HOH A:242	BINDING SITE FOR RESIDUE HEM A 200
02	AC2	SOFTWARE	HOH B:23 , LYS B:75 , SER B:82 , ALA B:83 , MET B:84 , TYR B:87 , TRP B:113 , ILE B:159 , ILE B:164 , TYR B:166 , TYR B:170 , THR B:172 , HOH B:207 , HOH B:259	BINDING SITE FOR RESIDUE HEM B 201
03	AC3	SOFTWARE	ASP A:133 , ASN A:134 , LYS A:135 , LYS A:136 , HOH A:191 , HOH A:266 , GOL B:9 , ARG B:140 , HOH B:216	BINDING SITE FOR RESIDUE SO4 A 1
04	AC4	SOFTWARE	GLU A:125 , LEU A:126 , ALA A:127 , HOH A:197 , HOH A:278	BINDING SITE FOR RESIDUE SO4 A 2
05	AC5	SOFTWARE	HOH A:56 , TYR A:119 , ASN A:123 , LYS A:156 , HOH A:286	BINDING SITE FOR RESIDUE GOL A 3
06	AC6	SOFTWARE	ALA A:179 , HOH A:261 , LYS B:114 , HIS B:158 , ASN B:167 , HOH B:219	BINDING SITE FOR RESIDUE GOL B 4
07	AC7	SOFTWARE	ASN A:165 , ASN B:120 , ALA B:121 , ASN B:122 , LYS B:151 , SER B:152	BINDING SITE FOR RESIDUE GOL B 5
08	AC8	SOFTWARE	HOH B:10 , ASP B:86 , MET B:88 , HIS B:90 , HOH B:253	BINDING SITE FOR RESIDUE GOL B 6
09	AC9	SOFTWARE	HIS A:158 , ASN A:167 , HOH A:218 , ALA B:179 , HOH B:234 , HOH B:281	BINDING SITE FOR RESIDUE GOL A 7
10	BC1	SOFTWARE	ASP A:86 , MET A:88 , HIS A:90 , HOH A:194	BINDING SITE FOR RESIDUE GOL A 8
11	BC2	SOFTWARE	SO4 A:1 , LYS B:114 , GLU B:115 , TYR B:116 , ARG B:140 , HOH B:216	BINDING SITE FOR RESIDUE GOL B 9
12	BC3	SOFTWARE	HOH A:44 , ASN A:109 , ALA A:137 , ASP A:138 , HOH A:216 , HOH A:221	BINDING SITE FOR RESIDUE GOL A 10
13	BC4	SOFTWARE	LYS B:75 , GLU B:80 , LYS B:81 , SER B:82 , ALA B:83 , HOH B:206 , HOH B:258	BINDING SITE FOR RESIDUE GOL B 11
14	BC5	SOFTWARE	HIS A:168 , HEM A:200 , HOH A:234 , HOH A:258	BINDING SITE FOR RESIDUE GOL A 12
15	BC6	SOFTWARE	LYS B:81 , ASP B:86 , HOH B:258	BINDING SITE FOR RESIDUE GOL B 13

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

Asymmetric Unit

No.	Residues
1	His A:90	-	Pro A:91
2	His B:90	-	Pro B:91

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NEAT	PS50978	NEAT domain profile.	ISDA_STAAN	62-184	2	A:62-184 B:62-184

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NEAT	PS50978	NEAT domain profile.	ISDA_STAAN	62-184	1	A:62-184 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NEAT	PS50978	NEAT domain profile.	ISDA_STAAN	62-184	1	- B:62-184

(no "Exon" information available for 3QZM)

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:124
 aligned with ISDA_STAAN | Q7A655 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:124
                                    70        80        90       100       110       120       130       140       150       160       170       180    
           ISDA_STAAN    61 VSQATSQPINFQVQKDGSSEKSHMDDYMQHPGKVIKQNNKYYFQTVLNNASFWKEYKFYNANNQELATTVVNDNKKADTRTINVAVEPGYKSLTTKVHIVVPQINYNHRYTTHLEFEKAIPTLA 184
               SCOP domains d3qzma_ A: automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.eeeee......hhhhhhh...eeeeee..eeeeeeeee....eeeeeee.....ee.eeeeeee....eeeeeeee.....eeeeeeeeeehhhheeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -NEAT  PDB: A:62-184 UniProt: 62-184                                                                                         PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qzm A  61 MSQATSQPINFQVQKDGSSEKSAMDDYMQHPGKVIKQNNKYYFQTVLNNASFWKEYKFYNANNQELATTVVNDNKKADTRTINVAVEPGYKSLTTKVHIVVPQINYNHRYTTHLEFEKAIPTLA 184
                                    70        80        90       100       110       120       130       140       150       160       170       180

Chain B from PDB  Type:PROTEIN  Length:123
 aligned with ISDA_STAAN | Q7A655 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:123
                                    71        81        91       101       111       121       131       141       151       161       171       181   
           ISDA_STAAN    62 SQATSQPINFQVQKDGSSEKSHMDDYMQHPGKVIKQNNKYYFQTVLNNASFWKEYKFYNANNQELATTVVNDNKKADTRTINVAVEPGYKSLTTKVHIVVPQINYNHRYTTHLEFEKAIPTLA 184
               SCOP domains d3qzmb_ B: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.eeeee......hhhhhhh...eeeeee..eeeeeeeee....eeeeeee.....ee.eeeeeee....eeeeeeee.....eeeeeeeeeehhhheeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE NEAT  PDB: B:62-184 UniProt: 62-184                                                                                         PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qzm B  62 SQATSQPINFQVQKDGSSEKSAMDDYMQHPGKVIKQNNKYYFQTVLNNASFWKEYKFYNANNQELATTVVNDNKKADTRTINVAVEPGYKSLTTKVHIVVPQINYNHRYTTHLEFEKAIPTLA 184
                                    71        81        91       101       111       121       131       141       151       161       171       181

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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: NEAT domain (14)

Protein domain: automated matches (9)

Staphylococcus aureus [TaxId: 158879] (5)

1a	d3qzma_	A:
1b	d3qzmb_	B:

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (ISDA_STAAN | Q7A655)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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.

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	Cis Peptide Bonds
		His A:90 - Pro A:91	[ RasMol ]
		His B:90 - Pro B:91	[ RasMol ]

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	3qzm
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	ISDA_STAAN \| Q7A655	:	3qzl 3qzn 3qzo 3qzp

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 15)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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