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(-) Description

Title :  CRYSTAL STRUCTURE OF A PERIPLASMIC HEME BINDING PROTEIN FROM SHIGELLA DYSENTERIAE
 
Authors :  W. W. Ho, H. Li, T. L. Poulos
Date :  07 Sep 07  (Deposition) - 09 Oct 07  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Periplasmic Binding Protein, Heme Transport, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. W. Ho, H. Li, S. Eakanunkul, Y. Tong, A. Wilks, M. Guo, T. L. Poulos
Holo- And Apo-Bound Structures Of Bacterial Periplasmic Heme-Binding Proteins.
J. Biol. Chem. V. 282 35796 2007
PubMed-ID: 17925389  |  Reference-DOI: 10.1074/JBC.M706761200

(-) Compounds

Molecule 1 - BACTERIAL HEME BINDING PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PSHU262
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: SHIGELLA DYSENTERIAE
    Organism Taxid: 622
    Strain: PSHU262

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1HEM-1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:30 , GLY A:31 , SER A:32 , GLU A:51 , THR A:52 , TYR A:67 , TRP A:87 , ARG A:111 , ALA A:169 , GLY A:170 , GLY A:171 , SER A:172 , SER A:181 , VAL A:182 , ALA A:183 , TYR A:201 , LEU A:257 , GLY A:258 , HOH A:605 , HOH A:677 , HOH A:722BINDING SITE FOR RESIDUE HEM A 600

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R7A)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Tyr A:55 -Pro A:56
2Gly A:91 -Pro A:92
3Val A:112 -Pro A:113
4Tyr B:55 -Pro B:56
5Gly B:91 -Pro B:92
6Val B:112 -Pro B:113
7Tyr C:55 -Pro C:56
8Gly C:91 -Pro C:92
9Val C:112 -Pro C:113
10Tyr D:55 -Pro D:56
11Gly D:91 -Pro D:92
12Val D:112 -Pro D:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R7A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R7A)

(-) Exons   (0, 0)

(no "Exon" information available for 2R7A)

(-) 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:255
 aligned with O70018_SHIDY | O70018 from UniProtKB/TrEMBL  Length:304

    Alignment length:255
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299     
         O70018_SHIDY    50 AERIVVAGGSLTELIYAMGAGERVVGVDETTSYPPETAKLPHIGYWKQLSSEGILSLRPDSVITWQDAGPQIVLDQLRAQKVNVVTLPRVPATLEQMYANIRQLAKTLQVPEQGDALVTQINQRLERVQQNVAAKKAPVKAMFILSAGGSAPQVAGKGSVADAILSLAGAENVATHQQYKSYSAESLIAANPEVIVVTSQMVDGDINRLRSIAGITHTAAWKNQRIITVDQNLILGMGPRIADVVESLHQQLWPQ 304
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeehhhhhhhhhhh.hhh.eeee......hhhhhhh.........hhhhhhh....eeeee....hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......eeeeee.......eee...hhhhhhhhhh..ee......ee..hhhhhhhhh..eeeeehhhhh.hhhhhhhh.hhhhhhhhhh..eeeehhhhhh....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r7a A  23 AERIVVAGGSLTELIYAMGAGERVVGVDETTSYPPETAKLPHIGYWKQLSSEGILSLRPDSVITWQDAGPQIVLDQLRAQKVNVVTLPRVPATLEQMYANIRQLAKTLQVPEQGDALVTQINQRLERVQQNVAAKKAPVKAMFILSAGGSAPQVAGKGSVADAILSLAGAENVATHQQYKSYSAESLIAANPEVIVVTSQMVDGDINRLRSIAGITHTAAWKNQRIITVDQNLILGMGPRIADVVESLHQQLWPQ 277
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272     


Chain B from PDB  Type:PROTEIN  Length:256
 aligned with O70018_SHIDY | O70018 from UniProtKB/TrEMBL  Length:304

    Alignment length:256
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298      
         O70018_SHIDY    49 AAERIVVAGGSLTELIYAMGAGERVVGVDETTSYPPETAKLPHIGYWKQLSSEGILSLRPDSVITWQDAGPQIVLDQLRAQKVNVVTLPRVPATLEQMYANIRQLAKTLQVPEQGDALVTQINQRLERVQQNVAAKKAPVKAMFILSAGGSAPQVAGKGSVADAILSLAGAENVATHQQYKSYSAESLIAANPEVIVVTSQMVDGDINRLRSIAGITHTAAWKNQRIITVDQNLILGMGPRIADVVESLHQQLWPQ 304
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeehhhhhhhhhhh.hhh.eee.......hhhhh...........hhhhhhh....eeeee....hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.......eee...hhhhhhhhhhheee......ee..hhhhhhhhh..eeeeehhhhh.hhhhhhhh.hhhhhhhhhh..eeeehhhhh.....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r7a B  22 AAERIVVAGGSLTELIYAMGAGERVVGVDETTSYPPETAKLPHIGYWKQLSSEGILSLRPDSVITWQDAGPQIVLDQLRAQKVNVVTLPRVPATLEQMYANIRQLAKTLQVPEQGDALVTQINQRLERVQQNVAAKKAPVKAMFILSAGGSAPQVAGKGSVADAILSLAGAENVATHQQYKSYSAESLIAANPEVIVVTSQMVDGDINRLRSIAGITHTAAWKNQRIITVDQNLILGMGPRIADVVESLHQQLWPQ 277
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271      


Chain C from PDB  Type:PROTEIN  Length:255
 aligned with O70018_SHIDY | O70018 from UniProtKB/TrEMBL  Length:304

    Alignment length:255
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299     
         O70018_SHIDY    50 AERIVVAGGSLTELIYAMGAGERVVGVDETTSYPPETAKLPHIGYWKQLSSEGILSLRPDSVITWQDAGPQIVLDQLRAQKVNVVTLPRVPATLEQMYANIRQLAKTLQVPEQGDALVTQINQRLERVQQNVAAKKAPVKAMFILSAGGSAPQVAGKGSVADAILSLAGAENVATHQQYKSYSAESLIAANPEVIVVTSQMVDGDINRLRSIAGITHTAAWKNQRIITVDQNLILGMGPRIADVVESLHQQLWPQ 304
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeehhhhhhhhhhh.hhh.eeee......hhhhh...........hhhhhhh....eeeee....hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.......eee...hhhhhhhhhhheee......ee..hhhhhhhhh..eeeeehhhhh.hhhhhhhh.hhhhhhhhhh..eeeehhhhh.....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r7a C  23 AERIVVAGGSLTELIYAMGAGERVVGVDETTSYPPETAKLPHIGYWKQLSSEGILSLRPDSVITWQDAGPQIVLDQLRAQKVNVVTLPRVPATLEQMYANIRQLAKTLQVPEQGDALVTQINQRLERVQQNVAAKKAPVKAMFILSAGGSAPQVAGKGSVADAILSLAGAENVATHQQYKSYSAESLIAANPEVIVVTSQMVDGDINRLRSIAGITHTAAWKNQRIITVDQNLILGMGPRIADVVESLHQQLWPQ 277
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272     


Chain D from PDB  Type:PROTEIN  Length:255
 aligned with O70018_SHIDY | O70018 from UniProtKB/TrEMBL  Length:304

    Alignment length:255
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299     
         O70018_SHIDY    50 AERIVVAGGSLTELIYAMGAGERVVGVDETTSYPPETAKLPHIGYWKQLSSEGILSLRPDSVITWQDAGPQIVLDQLRAQKVNVVTLPRVPATLEQMYANIRQLAKTLQVPEQGDALVTQINQRLERVQQNVAAKKAPVKAMFILSAGGSAPQVAGKGSVADAILSLAGAENVATHQQYKSYSAESLIAANPEVIVVTSQMVDGDINRLRSIAGITHTAAWKNQRIITVDQNLILGMGPRIADVVESLHQQLWPQ 304
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---Peripla_BP_2-2r7aD01 D:26-255                                                                                                                                                                                                         ---------------------- Pfam domains (1)
           Pfam domains (2) ---Peripla_BP_2-2r7aD02 D:26-255                                                                                                                                                                                                         ---------------------- Pfam domains (2)
           Pfam domains (3) ---Peripla_BP_2-2r7aD03 D:26-255                                                                                                                                                                                                         ---------------------- Pfam domains (3)
           Pfam domains (4) ---Peripla_BP_2-2r7aD04 D:26-255                                                                                                                                                                                                         ---------------------- Pfam domains (4)
         Sec.struct. author ...eeeehhhhhhhhhhh.hhh.eeee......hhhhh......hhhhhhhhhhhhh...eeeee....hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.......eee...hhhhhhhhhh..ee......ee..hhhhhhhhh..eeeeehhhhh.hhhhhhhh.hhhhhhhhhh..eeeehhhhh.....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r7a D  23 AERIVVAGGSLTELIYAMGAGERVVGVDETTSYPPETAKLPHIGYWKQLSSEGILSLRPDSVITWQDAGPQIVLDQLRAQKVNVVTLPRVPATLEQMYANIRQLAKTLQVPEQGDALVTQINQRLERVQQNVAAKKAPVKAMFILSAGGSAPQVAGKGSVADAILSLAGAENVATHQQYKSYSAESLIAANPEVIVVTSQMVDGDINRLRSIAGITHTAAWKNQRIITVDQNLILGMGPRIADVVESLHQQLWPQ 277
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2R7A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2R7A)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: Peripla_BP_2] (13)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (O70018_SHIDY | O70018)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  2r7a
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 Related Entries

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

UniProtKB/TrEMBL
        O70018_SHIDY | O70018: 2rg7

(-) Related Entries Specified in the PDB File

2r79