7WUM | pdb_00007wum

Crystal structure of UBR box from PRT6 (RDG pH 8.5)

• PDB DOI: https://doi.org/10.2210/pdb7WUM/pdb

• Classification: LIGASE
• Organism(s): Oryza sativa, Oryza sativa Japonica Group
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-02-08 Released: 2023-02-08 
• Deposition Author(s): Ho, M.C., Cao, C.C.
• Funding Organization(s): Academia Sinica (Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of UBR box from PRT6

Ho, M.C., Cao, C.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 8.46 kDa 
• Atom Count: 618 
• Modeled Residue Count: 73 
• Deposited Residue Count: 75 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-mer peptide	A [auth X]	3	Oryza sativa	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase	B [auth A]	72	Oryza sativa Japonica Group	Mutation(s): 0  Gene Names: Os01g0148000, OSNPB_010148000 EC: 2.3.2.27
UniProt
Find proteins for A0A0P0UY23 (Oryza sativa subsp. japonica) Explore A0A0P0UY23  Go to UniProtKB:  A0A0P0UY23

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.756	α = 90
b = 29.756	β = 90
c = 115.566	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-08 
Deposition Author(s): Ho, M.C., Cao, C.C.

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Funding Organization	Location	Grant Number
Academia Sinica (Taiwan)	Taiwan	--

Revision History  

• Version 1.0: 2023-02-08
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Data collection, Refinement description