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(-) Description

Title :  STRUCTURE BASED ENGINEERING OF STREPTAVIDIN MONOMER WITH A REDUCED BIOTIN DISSOCIATION RATE
 
Authors :  D. Demonte, E. J. Drake, K. Hong Lim, A. M. Gulick, S. Park
Date :  15 Mar 13  (Deposition) - 29 May 13  (Release) - 13 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
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:  B (1x),D (1x)
Keywords :  Beta Barrel, Engineered Streptavidin Variant, Biotin, Biotin-Binding Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Demonte, E. J. Drake, K. H. Lim, A. M. Gulick, S. Park
Structure-Based Engineering Of Streptavidin Monomer With A Reduced Biotin Dissociation Rate.
Proteins V. 81 1621 2013
PubMed-ID: 23670729  |  Reference-DOI: 10.1002/PROT.24320

(-) Compounds

Molecule 1 - STREPTAVIDIN/RHIZAVIDIN HYBRID
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 12-134
    Organism Scientific: STREPTOMYCES AVIDINII
    Organism Taxid: 1895

 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
Biological Unit 5 (1x):  B (1x) D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1BTN4Ligand/IonBIOTIN
2ZN9Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1BTN1Ligand/IonBIOTIN
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1BTN1Ligand/IonBIOTIN
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1BTN1Ligand/IonBIOTIN
2ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1BTN1Ligand/IonBIOTIN
2ZN-1Ligand/IonZINC ION
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
1BTN1Ligand/IonBIOTIN
2ZN-1Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:23 , SER A:27 , TYR A:43 , ASN A:45 , ALA A:47 , GLY A:49 , TRP A:79 , CYS A:86 , SER A:88 , THR A:90 , TRP A:108 , LEU A:110 , ASP A:128 , HOH A:308 , GLY B:12 , GLU B:14 , ZN B:204BINDING SITE FOR RESIDUE BTN A 201
02AC2SOFTWAREHIS A:87 , GLU A:113 , HIS C:87 , GLU C:113BINDING SITE FOR RESIDUE ZN A 202
03AC3SOFTWAREGLY A:12 , GLU A:14 , BTN B:201 , HOH B:347BINDING SITE FOR RESIDUE ZN A 203
04AC4SOFTWAREASP A:36 , HOH A:311 , HOH A:364BINDING SITE FOR RESIDUE ZN A 204
05AC5SOFTWAREGLY A:12 , GLU A:14 , ZN A:203 , ASN B:23 , SER B:27 , TYR B:43 , ASN B:45 , ALA B:47 , GLY B:49 , TRP B:79 , SER B:88 , THR B:90 , TRP B:92 , TRP B:108 , ASP B:128BINDING SITE FOR RESIDUE BTN B 201
06AC6SOFTWAREASP B:36 , ASN B:38 , HOH B:348BINDING SITE FOR RESIDUE ZN B 202
07AC7SOFTWAREGLU B:44 , HOH B:349 , HOH B:350 , ASP D:36BINDING SITE FOR RESIDUE ZN B 203
08AC8SOFTWAREBTN A:201 , GLY B:12 , GLU B:14 , HOH B:351BINDING SITE FOR RESIDUE ZN B 204
09AC9SOFTWAREASN C:23 , SER C:27 , TYR C:43 , ASN C:45 , ALA C:47 , GLY C:49 , TRP C:79 , SER C:88 , THR C:90 , TRP C:108 , ASP C:128 , ZN C:202BINDING SITE FOR RESIDUE BTN C 201
10BC1SOFTWAREBTN C:201BINDING SITE FOR RESIDUE ZN C 202
11BC2SOFTWAREASN D:23 , SER D:27 , TYR D:43 , ASN D:45 , ALA D:47 , THR D:48 , GLY D:49 , TRP D:79 , CYS D:86 , SER D:88 , THR D:90 , TRP D:108 , LEU D:110 , ASP D:128 , ZN D:202BINDING SITE FOR RESIDUE BTN D 201
12BC3SOFTWAREBTN D:201 , HOH D:356BINDING SITE FOR RESIDUE ZN D 202
13BC4SOFTWAREHIS B:87 , GLU B:113 , HIS D:87 , GLU D:113BINDING SITE FOR RESIDUE ZN D 203

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:50 -A:86
2B:50 -B:86
3C:50 -C:86
4D:50 -D:86

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JNJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JNJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JNJ)

(-) Exons   (0, 0)

(no "Exon" information available for 4JNJ)

(-) 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
                                                                                                                                                   
               SCOP domains d4jnja_ A: automated matches                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.eeeee....eeeeee....eeeeeee............eeeeeeee..eeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeeee....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 4jnj A  12 GAEAGITGTWYNQSGSTFTVTAGADGNLTGQYENRAQGTGCQNSPYTLTGRYNGTKLEWRVEWNNSTENCHSRTEWRGQYQGGAEARINTQWNLTYEGGSGPATEQGQDTFTKVK 134
                                    21        31        41      ||49  |     58  ||    76        86        96       106       119       129     
                                                              47A|  51A        61|                                          115|               
                                                               47B              70                                           119               


Chain B from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains d4jnjb_ B: automated matches                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhheeeee....eeeeee....eeeeeee...........eeeeeeeee..eeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeeee....eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4jnj B  12 GAEAGITGTWYNQSGSTFTVTAGADGNLTGQYENRAQGTGCQNSPYTLTGRYNGTKLEWRVEWNNSTENCHSRTEWRGQYQGGAEARINTQWNLTYEGGSGPATEQGQDTFTKV 133
                                    21        31        41      ||49  |     58  ||    76        86        96       106       119       129    
                                                              47A|  51A        61|                                          115|              
                                                               47B              70                                           119              


Chain C from PDB  Type:PROTEIN  Length:111
                                                                                                                                               
               SCOP domains d4jnjc_ C: automated matches                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....eeeeee....eeeeeee...........eeeeeeeee..eeeeeeeee....eeeeeeeeeeeeee...eeeeeeeeeeee....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 4jnj C  16 GITGTWYNQSGSTFTVTAGADGNLTGQYENRAQGTGCQNSPYTLTGRYNGTKLEWRVEWNNSTENCHSRTEWRGQYQGGAEARINTQWNLTYEGGSGPATEQGQDTFTKVK 134
                                    25        35        45  ||    52        70        80        90       100       110    || 123       133 
                                                          47A|  51A        61|                                          115|               
                                                           47B              70                                           119               


Chain D from PDB  Type:PROTEIN  Length:113
                                                                                                                                                 
               SCOP domains d4jnjd_ D: automated matches                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.....eeeeee....eeeeeee............eeeeeeee..eeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeeee....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 4jnj D  14 EAGITGTWYNQSGSTFTVTAGADGNLTGQYENRAQGTGCQNSPYTLTGRYNGTKLEWRVEWNNSTENCHSRTEWRGQYQGGAEARINTQWNLTYEGGSGPATEQGQDTFTKVK 134
                                    23        33        43    ||  51|       60||      78        88        98       108      |121       131   
                                                            47A|  51A        61|                                          115|               
                                                             47B              70                                           119
   Legend:   → Mismatch (orange background)
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  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 4JNJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JNJ)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4JNJ)

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