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(-) Description

Title :  STAPHYLOCOCCUS AUREUS ISDA NEAT DOMAIN IN COMPLEX WITH HEME, REDUCED CRYSTAL
 
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 :  1.95
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)
Keywords :  Heme, Transport, Iron, Uptake, Receptor, Cell Wall, Ferrous, 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

(-) Compounds

Molecule 1 - IRON-REGULATED SURFACE DETERMINANT PROTEIN A
    Chains: A, B, C, D
    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
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
    Organism Taxid: 158879
    Strain: N315
    Synonym: FUR-REGULATED PROTEIN A, STAPHYLOCOCCAL TRANSFERRIN-BINDING PROTEIN A

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:75 , SER A:82 , HIS A:83 , MET A:84 , TYR A:87 , PHE A:112 , TRP A:113 , ILE A:159 , ILE A:164 , TYR A:166 , TYR A:170 , THR A:172 , HOH A:187 , PRO B:162 , GLN B:163 , ILE B:164 , ASN B:165 , PRO C:162 , GLN C:163BINDING SITE FOR RESIDUE HEM A 200
2AC2SOFTWAREPRO A:162 , GLN A:163 , ASN A:165 , LYS B:75 , SER B:82 , HIS B:83 , MET B:84 , TYR B:87 , PHE B:112 , TRP B:113 , ILE B:159 , TYR B:166 , TYR B:170 , THR B:172 , HOH B:288BINDING SITE FOR RESIDUE HEM B 200
3AC3SOFTWARELYS C:75 , SER C:82 , HIS C:83 , MET C:84 , TYR C:87 , PHE C:112 , TRP C:113 , ILE C:159 , VAL C:161 , ILE C:164 , TYR C:166 , TYR C:170 , THR C:172 , HOH C:185 , HOH C:195 , HOH C:244 , ASP D:86 , TYR D:87 , HEM D:200BINDING SITE FOR RESIDUE HEM C 200
4AC4SOFTWARELYS C:114 , HIS C:158 , ASN C:167 , ARG C:169 , HOH C:369BINDING SITE FOR RESIDUE GOL C 2
5AC5SOFTWAREASP C:86 , TYR C:87 , HOH C:197 , HEM C:200 , HOH C:213 , HOH D:4 , HOH D:15 , LYS D:75 , SER D:82 , HIS D:83 , MET D:84 , TYR D:87 , TRP D:113 , ILE D:159 , VAL D:161 , ILE D:164 , TYR D:166 , TYR D:170 , THR D:172 , HOH D:185 , HOH D:212BINDING SITE FOR RESIDUE HEM D 200
6AC6SOFTWARELYS D:114 , HIS D:158 , ASN D:167BINDING SITE FOR RESIDUE GOL D 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1His A:90 -Pro A:91
2Asn A:98 -Asn A:99
3His B:90 -Pro B:91
4Asn B:99 -Lys B:100
5His C:90 -Pro C:91
6His D:90 -Pro D:91

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NEATPS50978 NEAT domain profile.ISDA_STAAN62-184
 		  2C:62-184
D:62-184
Biological Unit 1 (, 0)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NEATPS50978 NEAT domain profile.ISDA_STAAN62-184
 		  0-
-
Biological Unit 2 (, 0)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NEATPS50978 NEAT domain profile.ISDA_STAAN62-184
 		  0-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NEATPS50978 NEAT domain profile.ISDA_STAAN62-184
 		  1C:62-184
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NEATPS50978 NEAT domain profile.ISDA_STAAN62-184
 		  1-
D:62-184

(-) Exons   (0, 0)

(no "Exon" information available for 3QZO)

(-) Sequences/Alignments

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:121
 aligned with ISDA_STAAN | Q7A655 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:121
                                    73        83        93       103       113       123       133       143       153       163       173       183 
           ISDA_STAAN    64 ATSQPINFQVQKDGSSEKSHMDDYMQHPGKVIKQNNKYYFQTVLNNASFWKEYKFYNANNQELATTVVNDNKKADTRTINVAVEPGYKSLTTKVHIVVPQINYNHRYTTHLEFEKAIPTLA 184
               SCOP domains d3qzoa_ A: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.eeeee......hhhhhhh...eeeeee..eeeeeeeee....eeeeeee.....ee.eeeeeee....eeeeeeee.....eeeeeeeeeehhhheeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE NEAT  PDB: - UniProt: 62-184                                                                                              PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qzo A  64 ATSQPINFQVQKDGSSEKSHMDDYMQHPGKVIKQNNKYYFQTVLNNASFWKEYKFYNANNQELATTVVNDNKKADTRTINVAVEPGYKSLTTKVHIVVPQINYNHRYTTHLEFEKAIPTLA 184
                                    73        83        93       103       113       123       133       143       153       163       173       183 


Chain B from PDB  Type:PROTEIN  Length:121
 aligned with ISDA_STAAN | Q7A655 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:121
                                    73        83        93       103       113       123       133       143       153       163       173       183 
           ISDA_STAAN    64 ATSQPINFQVQKDGSSEKSHMDDYMQHPGKVIKQNNKYYFQTVLNNASFWKEYKFYNANNQELATTVVNDNKKADTRTINVAVEPGYKSLTTKVHIVVPQINYNHRYTTHLEFEKAIPTLA 184
               SCOP domains d3qzob_ B: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.eeeee......hhhhhhh...eeeee....eeeeeeee....eeeeeee.....ee.eeeeeee....eeeeeeee.....eeeeeeeeeehhhheeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE NEAT  PDB: - UniProt: 62-184                                                                                              PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qzo B  64 ATSQPINFQVQKDGSSEKSHMDDYMQHPGKVIKQNNKYYFQTVLNNASFWKEYKFYNANNQELATTVVNDNKKADTRTINVAVEPGYKSLTTKVHIVVPQINYNHRYTTHLEFEKAIPTLA 184
                                    73        83        93       103       113       123       133       143       153       163       173       183 


Chain C 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 d3qzoc_ C: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.eeeee......hhhhhhh...eeeeee..eeeeeeeee....eeeeeee.....ee.eeeeeee....eeeeeeee.....eeeeeeeeeehhhheeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE NEAT  PDB: C:62-184 UniProt: 62-184                                                                                         PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qzo C  62 SQATSQPINFQVQKDGSSEKSHMDDYMQHPGKVIKQNNKYYFQTVLNNASFWKEYKFYNANNQELATTVVNDNKKADTRTINVAVEPGYKSLTTKVHIVVPQINYNHRYTTHLEFEKAIPTLA 184
                                    71        81        91       101       111       121       131       141       151       161       171       181   


Chain D 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 d3qzod_ D: automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.eeeee......hhhhhhh...eeeeee..eeeeeeeee....eeeeeee.....ee.eeeeeee....eeeeeeee.....eeeeeeeeeehhhheeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -NEAT  PDB: D:62-184 UniProt: 62-184                                                                                         PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qzo D  61 MSQATSQPINFQVQKDGSSEKSHMDDYMQHPGKVIKQNNKYYFQTVLNNASFWKEYKFYNANNQELATTVVNDNKKADTRTINVAVEPGYKSLTTKVHIVVPQINYNHRYTTHLEFEKAIPTLA 184
                                    70        80        90       100       110       120       130       140       150       160       170       180
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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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  3qzo
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ISDA_STAAN | Q7A655: 3qzl 3qzm 3qzn 3qzp

(-) Related Entries Specified in the PDB File

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