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(-) Description

Title :  APO ISDH-NEAT3 IN SPACE GROUP P3121 AT A RESOLUTION OF 1.85 A
 
Authors :  N. T. Vu, J. M. M. Caaveiro, Y. Moriwaki, K. Tsumoto
Date :  26 Jun 12  (Deposition) - 26 Jun 13  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Biol. Unit 7:  A,B,C,D,E,F  (1x)
Keywords :  Neat Domain, Heme Binding, Heme Transport, Apo Form, Cell Wall, Heme- Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. T. Vu, Y. Moriwaki, J. M. M. Caaveiro, K. Tsumoto
Structure Of Heme Transport Protein Isdh-Neat3 From S. Aureus In Complex With Indium-Porphyrin
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IRON-REGULATED SURFACE DETERMINANT PROTEIN H
    ChainsA, B, C, D, E, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28
    Expression System StrainROSETTA2(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentNEAT DOMAIN, UNP RESIDUES 539-664
    GeneHARA, ISDH, ISDH-NEAT3, SASI, SAV1731
    Organism ScientificSTAPHYLOCOCCUS AUREUS
    Organism Taxid158878
    StrainMU50/ATCC 700699
    SynonymHAPTOGLOBIN RECEPTOR A, STAPHYLOCOCCUS AUREUS SURFACE PROTEIN I

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)A     
Biological Unit 2 (1x) B    
Biological Unit 3 (1x)  C   
Biological Unit 4 (1x)   D  
Biological Unit 5 (1x)    E 
Biological Unit 6 (1x)     F
Biological Unit 7 (1x)ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL6Ligand/IonGLYCEROL
3SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL-1Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (3, 6)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL3Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3SO4-1Ligand/IonSULFATE ION
Biological Unit 5 (2, 2)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 6 (1, 1)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2GOL-1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 7 (3, 14)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL6Ligand/IonGLYCEROL
3SO46Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:546 , LEU A:547 , HOH A:828 , HOH A:898 , HOH A:903 , ASN C:639 , LYS E:609 , HOH E:893BINDING SITE FOR RESIDUE SO4 A 701
02AC2SOFTWAREVAL A:569 , GLU A:570 , HIS A:571 , LYS A:589 , HOH A:813 , HOH A:860 , HOH C:889 , LYS E:612BINDING SITE FOR RESIDUE SO4 A 702
03AC3SOFTWARELYS A:609 , ASN A:639 , THR E:545 , ASP E:546 , LEU E:547BINDING SITE FOR RESIDUE ACT A 703
04AC4SOFTWAREASP B:591 , LYS B:595 , ASP B:596 , LEU B:597 , VAL B:604 , ARG B:616 , LEU B:618 , HOH B:831BINDING SITE FOR RESIDUE GOL B 701
05AC5SOFTWAREGLU C:549 , ASP C:654 , HOH C:873 , TYR F:646BINDING SITE FOR RESIDUE GOL C 701
06AC6SOFTWARETRP C:594 , ASP C:596 , LEU C:597 , VAL C:604 , ARG C:616 , HOH C:842BINDING SITE FOR RESIDUE GOL C 702
07AC7SOFTWAREASP C:625 , LYS C:626 , ALA C:627BINDING SITE FOR RESIDUE GOL C 703
08AC8SOFTWAREGLU C:570 , HIS C:571 , LYS C:589 , LYS C:612 , HOH C:818 , HOH C:882 , LYS E:589 , HOH E:904BINDING SITE FOR RESIDUE SO4 C 704
09AC9SOFTWARETHR C:545 , LYS C:609 , ARG C:616BINDING SITE FOR RESIDUE SO4 C 705
10BC1SOFTWARELYS C:587 , SER C:608 , LYS C:609 , ASP C:610 , SER C:615 , ARG C:616 , THR C:617 , HOH C:834BINDING SITE FOR RESIDUE ACT C 706
11BC2SOFTWAREASP D:591 , TRP D:594 , ASP D:596 , LEU D:597 , VAL D:604 , ARG D:616BINDING SITE FOR RESIDUE GOL D 701
12BC3SOFTWARETYR A:593 , ILE A:640 , TYR A:642 , VAL B:564 , TYR B:646 , GLN E:548 , GLU E:549 , HOH E:829 , HOH E:859BINDING SITE FOR RESIDUE GOL E 701
13BC4SOFTWARELYS A:589 , LYS A:612 , HOH A:846 , GLU E:570 , HIS E:571 , LYS E:589 , HOH E:842BINDING SITE FOR RESIDUE SO4 E 702
14BC5SOFTWAREGLU F:570 , HIS F:571 , LYS F:589 , HOH F:830 , HOH F:836BINDING SITE FOR RESIDUE SO4 F 701

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1His A:571 -Pro A:572
2His B:571 -Pro B:572
3His C:571 -Pro C:572
4His D:571 -Pro D:572
5His E:571 -Pro E:572
6His F:571 -Pro F:572

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 6)

Asymmetric Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NEATPS50978 NEAT domain profile.ISDH_STAAM105-232
345-471
543-660
 
 
 
 
 
  6-
-
A:543-657
B:543-656
C:543-656
D:543-656
E:543-655
F:543-655
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NEATPS50978 NEAT domain profile.ISDH_STAAM105-232
345-471
543-660
 
 
 
 
 
  1-
-
A:543-657
-
-
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NEATPS50978 NEAT domain profile.ISDH_STAAM105-232
345-471
543-660
 
 
 
 
 
  1-
-
-
B:543-656
-
-
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NEATPS50978 NEAT domain profile.ISDH_STAAM105-232
345-471
543-660
 
 
 
 
 
  1-
-
-
-
C:543-656
-
-
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NEATPS50978 NEAT domain profile.ISDH_STAAM105-232
345-471
543-660
 
 
 
 
 
  1-
-
-
-
-
D:543-656
-
-
Biological Unit 5 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NEATPS50978 NEAT domain profile.ISDH_STAAM105-232
345-471
543-660
 
 
 
 
 
  1-
-
-
-
-
-
E:543-655
-
Biological Unit 6 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NEATPS50978 NEAT domain profile.ISDH_STAAM105-232
345-471
543-660
 
 
 
 
 
  1-
-
-
-
-
-
-
F:543-655
Biological Unit 7 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NEATPS50978 NEAT domain profile.ISDH_STAAM105-232
345-471
543-660
 
 
 
 
 
  6-
-
A:543-657
B:543-656
C:543-656
D:543-656
E:543-655
F:543-655

(-) Exons   (0, 0)

(no "Exon" information available for 3VUA)

(-) 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:115
 aligned with ISDH_STAAM | Q931P4 from UniProtKB/Swiss-Prot  Length:891

    Alignment length:115
                                   552       562       572       582       592       602       612       622       632       642       652     
           ISDH_STAAM   543 QLTDLQEAHFVVFESEENSESVMDGFVEHPFYTATLNGQKYVVMKTKDDSYWKDLIVEGKRVTTVSKDPKNNSRTLIFPYIPDKAVYNAIVKVVVANIGYEGQYHVRIINQDINT 657
               SCOP domains d3vuaa_ 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:543-657 UniProt: 543-660                                                                               PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 3vua A 543 QLTDLQEAHFVVFESEENSESVMDGFVEHPFYTATLNGQKYVVMKTKDDSYWKDLIVEGKRVTTVSKDPKNNSRTLIFPYIPDKAVYNAIVKVVVANIGYEGQYHVRIINQDINT 657
                                   552       562       572       582       592       602       612       622       632       642       652     

Chain B from PDB  Type:PROTEIN  Length:114
 aligned with ISDH_STAAM | Q931P4 from UniProtKB/Swiss-Prot  Length:891

    Alignment length:114
                                   552       562       572       582       592       602       612       622       632       642       652    
           ISDH_STAAM   543 QLTDLQEAHFVVFESEENSESVMDGFVEHPFYTATLNGQKYVVMKTKDDSYWKDLIVEGKRVTTVSKDPKNNSRTLIFPYIPDKAVYNAIVKVVVANIGYEGQYHVRIINQDIN 656
               SCOP domains d3vuab_ 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: B:543-656 UniProt: 543-660                                                                              PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3vua B 543 QLTDLQEAHFVVFESEENSESVMDGFVEHPFYTATLNGQKYVVMKTKDDSYWKDLIVEGKRVTTVSKDPKNNSRTLIFPYIPDKAVYNAIVKVVVANIGYEGQYHVRIINQDIN 656
                                   552       562       572       582       592       602       612       622       632       642       652    

Chain C from PDB  Type:PROTEIN  Length:114
 aligned with ISDH_STAAM | Q931P4 from UniProtKB/Swiss-Prot  Length:891

    Alignment length:114
                                   552       562       572       582       592       602       612       622       632       642       652    
           ISDH_STAAM   543 QLTDLQEAHFVVFESEENSESVMDGFVEHPFYTATLNGQKYVVMKTKDDSYWKDLIVEGKRVTTVSKDPKNNSRTLIFPYIPDKAVYNAIVKVVVANIGYEGQYHVRIINQDIN 656
               SCOP domains d3vuac_ C: automated matches                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee.eeeee......hhhhhhh...eeeeee..eeeeeee..hhh.eeeeee..ee.eeeeee....eeeeeee......eeeeeeeeeehhh.eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE NEAT  PDB: C:543-656 UniProt: 543-660                                                                              PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3vua C 543 QLTDLQEAHFVVFESEENSESVMDGFVEHPFYTATLNGQKYVVMKTKDDSYWKDLIVEGKRVTTVSKDPKNNSRTLIFPYIPDKAVYNAIVKVVVANIGYEGQYHVRIINQDIN 656
                                   552       562       572       582       592       602       612       622       632       642       652    

Chain D from PDB  Type:PROTEIN  Length:114
 aligned with ISDH_STAAM | Q931P4 from UniProtKB/Swiss-Prot  Length:891

    Alignment length:114
                                   552       562       572       582       592       602       612       622       632       642       652    
           ISDH_STAAM   543 QLTDLQEAHFVVFESEENSESVMDGFVEHPFYTATLNGQKYVVMKTKDDSYWKDLIVEGKRVTTVSKDPKNNSRTLIFPYIPDKAVYNAIVKVVVANIGYEGQYHVRIINQDIN 656
               SCOP domains d3vuad_ D: 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: D:543-656 UniProt: 543-660                                                                              PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3vua D 543 QLTDLQEAHFVVFESEENSESVMDGFVEHPFYTATLNGQKYVVMKTKDDSYWKDLIVEGKRVTTVSKDPKNNSRTLIFPYIPDKAVYNAIVKVVVANIGYEGQYHVRIINQDIN 656
                                   552       562       572       582       592       602       612       622       632       642       652    

Chain E from PDB  Type:PROTEIN  Length:113
 aligned with ISDH_STAAM | Q931P4 from UniProtKB/Swiss-Prot  Length:891

    Alignment length:113
                                   552       562       572       582       592       602       612       622       632       642       652   
           ISDH_STAAM   543 QLTDLQEAHFVVFESEENSESVMDGFVEHPFYTATLNGQKYVVMKTKDDSYWKDLIVEGKRVTTVSKDPKNNSRTLIFPYIPDKAVYNAIVKVVVANIGYEGQYHVRIINQDI 655
               SCOP domains d3vuae_ E: 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: E:543-655 UniProt: 543-660                                                                             PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 3vua E 543 QLTDLQEAHFVVFESEENSESVMDGFVEHPFYTATLNGQKYVVMKTKDDSYWKDLIVEGKRVTTVSKDPKNNSRTLIFPYIPDKAVYNAIVKVVVANIGYEGQYHVRIINQDI 655
                                   552       562       572       582       592       602       612       622       632       642       652   

Chain F from PDB  Type:PROTEIN  Length:113
 aligned with ISDH_STAAM | Q931P4 from UniProtKB/Swiss-Prot  Length:891

    Alignment length:113
                                   552       562       572       582       592       602       612       622       632       642       652   
           ISDH_STAAM   543 QLTDLQEAHFVVFESEENSESVMDGFVEHPFYTATLNGQKYVVMKTKDDSYWKDLIVEGKRVTTVSKDPKNNSRTLIFPYIPDKAVYNAIVKVVVANIGYEGQYHVRIINQDI 655
               SCOP domains d3vuaf_ F: automated matches                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeeee......hhhhhhh....eeeee..eeeeeee......eeeeee..ee.eeeee......eeeeee......eeeeeeeeeehhh.eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE NEAT  PDB: F:543-655 UniProt: 543-660                                                                             PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 3vua F 543 QLTDLQEAHFVVFESEENSESVMDGFVEHPFYTATLNGQKYVVMKTKDDSYWKDLIVEGKRVTTVSKDPKNNSRTLIFPYIPDKAVYNAIVKVVVANIGYEGQYHVRIINQDI 655
                                   552       562       572       582       592       602       612       622       632       642       652   

   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, 6)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (ISDH_STAAM | Q931P4)
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.

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  ISDH_STAAM | Q931P4
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        ISDH_STAAM | Q931P42e7d 2z6f 3qug 3quh 3vtm

(-) Related Entries Specified in the PDB File

2e7d APO ISDH-NEAT3 IN SPACE GROUP H32 AT 2.2 A
2z6f ISDH-NEAT3 WITH FE(III)PPIX BOUND
3qug ISDH-NEAT3 WITH GA(III)PPIX BOUND
3quh ISDH-NEAT3 WITH MN(III)PPIX BOUND