3WYP | pdb_00003wyp

Crystal structure of wild-type core streptavidin in complex with D-biotin/biotin-D-sulfoxide at 1.3 A resolution

PDB DOI: https://doi.org/10.2210/pdb3WYP/pdb

Classification: BIOTIN BINDING PROTEIN
Organism(s): Streptomyces avidinii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-09-05 Released: 2014-12-24
Deposition Author(s): Kawato, T., Mizohata, E., Meshizuka, T., Doi, H., Kawamura, T., Matsumura, H., Yumura, K., Tsumoto, K., Kodama, T., Inoue, T., Sugiyama, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.179 (Depositor), 0.187 (DCC)
R-Value Work:
0.131 (Depositor), 0.142 (DCC)
R-Value Observed:
0.133 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of streptavidin mutant with low immunogenicity.

Kawato, T., Mizohata, E., Meshizuka, T., Doi, H., Kawamura, T., Matsumura, H., Yumura, K., Tsumoto, K., Kodama, T., Inoue, T., Sugiyama, A.

(2015) J Biosci Bioeng 119: 642-647

PubMed: 25434833 Search on PubMed
DOI: https://doi.org/10.1016/j.jbiosc.2014.10.025
Primary Citation Related Structures:
3WYP, 3WYQ

PubMed Abstract:
We previously created a low-immunogenic core streptavidin mutant No. 314 (LISA-314) by replacing six amino-acid residues for use as a delivery tool for an antibody multistep pre-targeting process (Yumura et al., Protein Sci., 22, 213-221, 2013). Here, we performed high-resolution X-ray structural analyses of LISA-314 and wild-type streptavidin to investigate the effect of substitutions on the protein function and the three-dimensional structure. LISA-314 forms a tetramer in the same manner as wild-type streptavidin. The binding mode of d-biotin in LISA-314 is also completely identical to that in wild-type streptavidin, and conformational changes were observed mostly at the side chains of substituted sites. Any large conformational changes corresponding to the reduction of B factors around the substituted sites were not observed. These results demonstrated the LISA-314 acquired low immunogenicity without losing structural properties of original wild-type streptavidin.

Organizational Affiliation

Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.

Macromolecule Content

Total Structure Weight: 55.25 kDa
Atom Count: 4,313
Modeled Residue Count: 486
Deposited Residue Count: 508
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A, B, C [auth D], D [auth C]	127	Streptomyces avidinii	Mutation(s): 0
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629 Go to UniProtKB: P22629
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22629
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BSO Query on BSO Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain I [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain I [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain I [auth B]	I [auth B], Q [auth C]	BIOTIN-D-SULFOXIDE C₁₀ H₁₆ N₂ O₄ S KCSKCIQYNAOBNQ-OKPRWBIXSA-N		Interactions Focus chain I [auth B] Focus chain Q [auth C] Interactions & Density Focus chain I [auth B] Focus chain Q [auth C]
BTN Query on BTN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain M [auth D] mmCIF format, chain E [auth A] mmCIF format, chain M [auth D]	E [auth A], M [auth D]	BIOTIN C₁₀ H₁₆ N₂ O₃ S YBJHBAHKTGYVGT-ZKWXMUAHSA-N		Interactions Focus chain E [auth A] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain M [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain L [auth B] MOL2 format, chain T [auth C] MOL2 format, chain L [auth B] mmCIF format, chain T [auth C] mmCIF format, chain L [auth B]	L [auth B], T [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L [auth B] Focus chain T [auth C] Interactions & Density Focus chain L [auth B] Focus chain T [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain N [auth D] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain N [auth D] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain N [auth D] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] J [auth B] K [auth B] F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], N [auth D], O [auth D], P [auth D], R [auth C], S [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D] Focus chain R [auth C] Focus chain S [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
BTN	BindingDB: 3WYP	Kd: 0 (nM) from 1 assay(s)
BTN	BindingDB: 3WYP	ΔG: min: -1.23e+2, max: -6.69e+1 (kJ/mol) from 12 assay(s)