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(-) Description

Title :  STREPTAVIDIN MUTANT S27A WITH BIOTIN AT 1.6A RESOLUTION
 
Authors :  I. Le Trong, S. Freitag, L. A. Klumb, V. Chu, P. S. Stayton, R. E. Stenkamp
Date :  25 Nov 02  (Deposition) - 02 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Homotetramer, Biotin-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Le Trong, S. Freitag, L. A. Klumb, V. Chu, P. S. Stayton, R. E. Stenkamp
Structural Studies Of Hydrogen Bonds In The High-Affinity Streptavidin-Biotin Complex: Mutations Of Amino Acids Interacting With The Ureido Oxygen Of Biotin.
Acta Crystallogr. , Sect. D V. 59 1567 2003
PubMed-ID: 12925786  |  Reference-DOI: 10.1107/S0907444903014562
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - STREPTAVIDIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET21A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: CORE STREPTAVIDIN, RESIDUES 13-139
    Gene: CORE STREPTAVIDIN
    Mutation: YES
    Organism Scientific: STREPTOMYCES AVIDINII
    Organism Taxid: 1895

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1BTN4Ligand/IonBIOTIN

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:23 , LEU A:25 , ALA A:27 , TYR A:43 , SER A:45 , VAL A:47 , ASN A:49 , TRP A:79 , SER A:88 , THR A:90 , TRP A:108 , ASP A:128 , HOH A:6147 , HOH A:6444BINDING SITE FOR RESIDUE BTN A 5100
2AC2SOFTWAREASN B:23 , LEU B:25 , ALA B:27 , TYR B:43 , SER B:45 , VAL B:47 , ASN B:49 , TRP B:79 , SER B:88 , THR B:90 , TRP B:108 , ASP B:128 , HOH B:6050BINDING SITE FOR RESIDUE BTN B 5200
3AC3SOFTWAREASN C:23 , LEU C:25 , ALA C:27 , TYR C:43 , SER C:45 , VAL C:47 , ASN C:49 , TRP C:79 , SER C:88 , THR C:90 , TRP C:108 , ASP C:128 , HOH C:6001 , HOH C:6341BINDING SITE FOR RESIDUE BTN C 5300
4AC4SOFTWAREASN D:23 , LEU D:25 , ALA D:27 , TYR D:43 , SER D:45 , VAL D:47 , ASN D:49 , TRP D:79 , SER D:88 , THR D:90 , TRP D:108 , ASP D:128 , HOH D:6006 , HOH D:6197BINDING SITE FOR RESIDUE BTN D 5400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N9M)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala C:137 -Ala C:138

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N9M)

(-) PROSITE Motifs  (2, 6)

Asymmetric/Biological Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AVIDIN_2PS51326 Avidin-like domain profile.SAV_STRAV37-159
 		  2C:13-135
D:13-135
2AVIDIN_1PS00577 Avidin-like domain signature.SAV_STRAV142-156
 
 
 		  4A:118-132
B:118-132
C:118-132
D:118-132

(-) Exons   (0, 0)

(no "Exon" information available for 1N9M)

(-) Sequences/Alignments

Asymmetric/Biological 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 SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:121
                                    47        57        67        77        87        97       107       117       127       137       147       157 
            SAV_STRAV    38 EAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVK 158
               SCOP domains d1n9ma_ A: Streptavidin                                                                                                   SCOP domains
               CATH domains 1n9mA00 A:14-134  [code=2.40.128.30, no name defined]                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.....eeeeee....eeeeeee.........eeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee..hhhhhhh.eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) AVIDIN_2  PDB: - UniProt: 37-159                                                                                          PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------AVIDIN_1       -- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n9m A  14 EAGITGTWYNQLGATFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVK 134
                                    23        33        43        53        63        73        83        93       103       113       123       133 


Chain B from PDB  Type:PROTEIN  Length:117
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:117
                                    49        59        69        79        89        99       109       119       129       139       149       
            SAV_STRAV    40 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTK 156
               SCOP domains d1n9mb_ B: Streptavidin                                                                                               SCOP domains
               CATH domains 1n9mB00 B:16-132  [code=2.40.128.30, no name defined]                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....eeeeee....eeeeeee.........eeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee..hhhhhhh.eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) AVIDIN_2  PDB: - UniProt: 37-159                                                                                      PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------AVIDIN_1        PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1n9m B  16 GITGTWYNQLGATFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTK 132
                                    25        35        45        55        65        75        85        95       105       115       125       


Chain C from PDB  Type:PROTEIN  Length:127
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:127
                                    46        56        66        76        86        96       106       116       126       136       146       156       
            SAV_STRAV    37 AEAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKPSAAS 163
               SCOP domains d1n9mc_ C: Streptavidin                                                                                                         SCOP domains
               CATH domains 1n9mC00 C:13-139  [code=2.40.128.30, no name defined]                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.....eeeeee....eeeeeee.........eeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee..hhhhhhh.eeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) AVIDIN_2  PDB: C:13-135 UniProt: 37-159                                                                                    ---- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------AVIDIN_1       ------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n9m C  13 AEAGITGTWYNQLGATFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKPSAAS 139
                                    22        32        42        52        62        72        82        92       102       112       122       132       


Chain D from PDB  Type:PROTEIN  Length:123
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:123
                                    46        56        66        76        86        96       106       116       126       136       146       156   
            SAV_STRAV    37 AEAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKP 159
               SCOP domains d1n9md_ D: Streptavidin                                                                                                     SCOP domains
               CATH domains 1n9mD00 D:13-135  [code=2.40.128.30, no name defined]                                                                       CATH domains
           Pfam domains (1) --Avidin-1n9mD01 D:15-132                                                                                               --- Pfam domains (1)
           Pfam domains (2) --Avidin-1n9mD02 D:15-132                                                                                               --- Pfam domains (2)
           Pfam domains (3) --Avidin-1n9mD03 D:15-132                                                                                               --- Pfam domains (3)
           Pfam domains (4) --Avidin-1n9mD04 D:15-132                                                                                               --- Pfam domains (4)
         Sec.struct. author ......eeeee....eeeeee....eeeeeee.........eeeeeee..........eeeeeeeeee....eeeeeeeeeeee......eeeeeeeeee..hhhhhhh.eeee..eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) AVIDIN_2  PDB: D:13-135 UniProt: 37-159                                                                                     PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------AVIDIN_1       --- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n9m D  13 AEAGITGTWYNQLGATFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKP 135
                                    22        32        42        52        62        72        82        92       102       112       122       132
   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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Avidin] (113)
(-)
Family: Avidin (113)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (SAV_STRAV | P22629)
cellular component
    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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  1n9m
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 Related Entries

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

UniProtKB/Swiss-Prot
        SAV_STRAV | P22629: 1df8 1hqq 1hxl 1hxz 1hy2 1i9h 1kff 1kl3 1kl4 1kl5 1lcv 1lcw 1lcz 1luq 1mep 1mk5 1mm9 1moy 1n43 1n4j 1n7y 1n9y 1nbx 1nc9 1ndj 1nqm 1pts 1rst 1rsu 1rxh 1rxj 1rxk 1sld 1sle 1slf 1slg 1sre 1srf 1srg 1srh 1sri 1srj 1stp 1str 1sts 1swa 1swb 1swc 1swd 1swe 1swf 1swg 1swh 1swj 1swk 1swl 1swn 1swo 1swp 1swq 1swr 1sws 1swt 1swu 1vwa 1vwb 1vwc 1vwd 1vwe 1vwf 1vwg 1vwh 1vwi 1vwj 1vwk 1vwl 1vwm 1vwn 1vwo 1vwp 1vwq 1vwr 2bc3 2f01 2g5l 2gh7 2iza 2izb 2izc 2izd 2ize 2izf 2izg 2izh 2izi 2izj 2izk 2izl 2qcb 2rta 2rtb 2rtc 2rtd 2rte 2rtf 2rtg 2rth 2rti 2rtj 2rtk 2rtl 2rtm 2rtn 2rto 2rtp 2rtq 2rtr 2wpu 2y3e 2y3f 3mg5 3pk2 3rdm 3rdo 3rdq 3rds 3rdu 3rdx 3re5 3re6 3ry1 3ry2 3t6f 3t6l 3wyp 3wyq 3wzn 3wzo 3wzp 3wzq 3x00 4bx5 4bx6 4bx7 4cpe 4cpf 4cph 4cpi 4dne 4ekv 4gd9 4gda 4gjs 4gjv 4irw 4jo6 4oka 4y59 4y5d 4yvb 5b5f 5b5g 5cse 5f2b 5jd2 5k49 5k67 5k68 5l3y 5to2

(-) Related Entries Specified in the PDB File

1n43 STREPTAVIDIN MUTANT N23A WITH BIOTIN AT 1.89A RESOLUTION
1n4j STREPTAVIDIN MUTANT N23A AT 2.18A RESOLUTION
1n7y STREPTAVIDIN MUTANT N23E AT 1.96A RESOLUTION