8BDU | pdb_00008bdu

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

• PDB DOI: https://doi.org/10.2210/pdb8BDU/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-10-20 Released: 2023-08-16 
• Deposition Author(s): Kolenko, P., Mikulecky, P., Pham, P.N., Schneider, B.
• Funding Organization(s): Ministry of Education, Youth and Sports of the Czech Republic

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 
  0.255 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

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.

(2023) J Appl Crystallogr 56: 1261-1266

• PubMed: 37555209 
• DOI: https://doi.org/10.1107/S160057672300479X
• Primary Citation Related Structures: 
  8BDU


• PubMed Abstract: 
  

  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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Organizational Affiliation: 
• Czech Technical University in Prague, Brehova 7, Prague 115 19, Czech Republic.
Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Průmyslová 595, Vestec 25250, Czech Republic.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.15 kDa 
• Atom Count: 2,071 
• Modeled Residue Count: 266 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PIH1 domain-containing protein 1	A, B	152	Homo sapiens	Mutation(s): 10  Gene Names: PIH1D1, NOP17
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWS0 (Homo sapiens) Explore Q9NWS0  Go to UniProtKB:  Q9NWS0
PHAROS:  Q9NWS0 GTEx:  ENSG00000104872

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free:  0.255 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.131	α = 90
b = 123.131	β = 90
c = 190.106	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-16 
Deposition Author(s): Kolenko, P., Mikulecky, P., Pham, P.N., Schneider, B.

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Funding Organization	Location	Grant Number
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	CZ.02.1.01/0.0/0.0/16_019/0000778

Revision History  

• Version 1.0: 2023-08-16
  Type: Initial release
  
• Version 1.1: 2023-08-23
  Changes: Database references
• Version 1.2: 2026-03-04
  Changes: Refinement description, Structure summary