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(-) Description

Title :  CRYSTAL STRUCTURE OF R7-2 STREPTAVIDIN COMPLEXED WITH BIOTIN
 
Authors :  V. N Malashkevich, M. Magalhaes, C. M. Czecster, R. Guan, M. Levy, S. C.
Date :  01 Apr 11  (Deposition) - 06 Jul 11  (Release) - 06 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Streptavidin Variants, Improved Desthiobiotin Binding, Opened Loop Destabilization, Biotin Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. L. Magalhaes, C. M. Czekster, R. Guan, V. N. Malashkevich, S. C. Almo M. Levy
Evolved Streptavidin Mutants Reveal Key Role Of Loop Residu In High-Affinity Binding.
Protein Sci. V. 20 1145 2011
PubMed-ID: 21520321  |  Reference-DOI: 10.1002/PRO.642

(-) Compounds

Molecule 1 - STREPTAVIDIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCR2.1-TOPO
    Expression System Strain: BL21(DE3)CODON+RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 37-164
    Mutation: YES
    Organism Scientific: STREPTOMYCES AVIDINII
    Organism Taxid: 1895

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1BTN1Ligand/IonBIOTIN
2GOL2Ligand/IonGLYCEROL
3NI1Ligand/IonNICKEL (II) ION
4SO41Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:-6 , HIS A:-5 , HIS A:-3 , ASN A:23 , LEU A:25 , SER A:27 , TYR A:43 , SER A:45 , VAL A:47 , ASN A:49 , TRP A:79 , ALA A:86 , SER A:88 , SER A:90 , ASP A:128 , NI A:301 , SO4 A:302BINDING SITE FOR RESIDUE BTN A 300
2AC2SOFTWAREHIS A:-6 , HIS A:-3 , HIS A:-5 , BTN A:300 , SO4 A:302BINDING SITE FOR RESIDUE NI A 301
3AC3SOFTWAREHIS A:-6 , HIS A:-4 , HIS A:-5 , HIS A:-3 , GLY A:48 , ASN A:49 , LYS A:121 , BTN A:300 , NI A:301BINDING SITE FOR RESIDUE SO4 A 302
4AC4SOFTWAREGLN A:24 , LEU A:25 , ALA A:119 , TRP A:120 , GLY A:126 , HIS A:127 , HOH A:151 , HOH A:173 , HOH A:225 , HOH A:310BINDING SITE FOR RESIDUE GOL A 303
5AC5SOFTWAREHIS A:-6 , HIS A:-5 , HIS A:-4 , SER A:112 , LYS A:121 , HOH A:305BINDING SITE FOR RESIDUE GOL A 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3RDO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3RDO)

(-) 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    
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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:129
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:129
                                    40        50        60        70        80        90       100       110       120       130       140       150         
            SAV_STRAV    31 KAQVSAAEAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKP 159
               SCOP domains -----d3rdoa1 A:12-135 automated matches                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------Avidin-3rdoA01 A:15-132                                                                                               --- Pfam domains
         Sec.struct. author .....hhhhhhheeeee....eeeeee....eeeeeee.........eeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee.....hhhh.eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------AVIDIN_2  PDB: A:13-135 UniProt: 37-159                                                                                     PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------AVIDIN_1       --- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rdo A  -6 HHHHSTAEAGITGTWYNQLGSTLIVTAGADGALTGTYESAVGNAEGSYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSASTWSGQYVGGAEARINTQVLTTSGTTEANAWKSTLVGHDTFTKVKP 135
                                ||  16        26        36        46        56        66        76        86        96       106       116       126         
                               -2|                                                                                                                           
                                12
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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  (1, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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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 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 1n9m 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 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

3rdm 3rdq 3rds 3rdu 3rdx 3re5 3re6