ISDA

Deposition Date 2022-10-20

Release Date 2023-08-16

Last Version Date 2023-08-23

Entry Detail

PDB ID:

8BDU

Keywords:

PROTEIN BINDING

Title:

H33 variant of DoBi scaffold based on PIH1D1 N-terminal domain

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli BL21(DE3)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.47 Å

R-Value Free:

0.25

R-Value Work:

0.21

R-Value Observed:

0.22

Space Group:

I 41 2 2

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:PIH1 domain-containing protein 1
Gene (Uniprot):PIH1D1
Chain IDs:A, B
Chain Length:152
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:Q9NWS0 Pfam ID:PF08190

Ligand Molecules

Primary Citation

Diffraction anisotropy and paired refinement: crystal structure of H33, a protein binder to interleukin 10.

Kolenko, P, Mikulecky, P, Pham, P.N, Maly, M, Schneider, B.Show

J.Appl.Crystallogr. 56 1261 1266 (2023)

PMID: 37555209 DOI: 10.1107/S160057672300479X

Abstact

Binder H33 is a small protein binder engineered by ribosome display to bind human interleukin 10. Crystals of binder H33 display severe diffraction anisotropy. A set of data files with correction for diffraction anisotropy based on different local signal-to-noise ratios was prepared. Paired refinement was used to find the optimal anisotropic high-resolution diffraction limit of the data: 3.13-2.47 Å. The structure of binder H33 belongs to the 2% of crystal structures with the highest solvent content in the Protein Data Bank.

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Primary Citation of related structures