5YOX | pdb_00005yox

HD domain-containing protein YGK1(YGL101W)

• PDB DOI: https://doi.org/10.2210/pdb5YOX/pdb

• Classification: LYASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-10-31 Released: 2018-11-21 
• Deposition Author(s): Yang, J., Wang, F., Gao, Z., Zhou, K., Liu, Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 
  0.245 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

HD domain-containing protein YGK1(YGL101W)

Yang, J., Wang, F., Zhou, K., Gao, Z., Liu, Q.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 205.44 kDa 
• Atom Count: 11,919 
• Modeled Residue Count: 1,406 
• Deposited Residue Count: 1,720 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HD domain-containing protein YGL101W	A, B, C, D, E, F, G, H	215	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: YGL101W EC: 3.1.3.89
UniProt
Find proteins for P53144 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53144  Go to UniProtKB:  P53144

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free:  0.245 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.633	α = 90
b = 142.178	β = 89.99
c = 112.266	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SHELXCD	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-11-21 
Deposition Author(s): Yang, J., Wang, F., Gao, Z., Zhou, K., Liu, Q.

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Funding Organization	Location	Grant Number
	China	--

Revision History  

• Version 1.0: 2018-11-21
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary