5YUG

AtVAL1 PHD-Like domain in the P31 space group

• PDB DOI: https://doi.org/10.2210/pdb5YUG/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-11-22 Released: 2018-05-02 
• Deposition Author(s): Zhang, M.M., Wu, B.X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.254 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 

Literature

AtVAL1 PHD-Like domain in the P31 space group

Zhang, M.M., Wu, B.X.

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)

Macromolecule Content

• Total Structure Weight: 50.01 kDa 
• Atom Count: 3,127 
• Modelled Residue Count: 388 
• Deposited Residue Count: 440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B3 domain-containing transcription repressor VAL1	A, B, C [auth E], D [auth G]	110	Arabidopsis thaliana	Mutation(s): 0  Gene Names: VAL1, HSI2, At2g30470, T6B20.17
UniProt
Find proteins for Q8W4L5 (Arabidopsis thaliana) Explore Q8W4L5  Go to UniProtKB:  Q8W4L5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	H [auth A], L [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], M [auth E], N [auth E], O [auth E], P [auth G], Q [auth G], R [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.254 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.228	α = 90
b = 52.228	β = 90
c = 121.674	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELXCD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-02 
Deposition Author(s): Zhang, M.M., Wu, B.X.

Revision History  

• Version 1.0: 2018-05-02
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Data collection, Database references, Source and taxonomy, Structure summary
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references