6K9N

Rice_OTUB_like_catalytic domain

• PDB DOI: https://doi.org/10.2210/pdb6K9N/pdb

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


• Deposited: 2019-06-17 Released: 2020-06-24 
• Deposition Author(s): Lu, L.N., Liu, L., Wang, F.
• Funding Organization(s): The National Key Research and Development Program of China, National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.217 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Literature

Met1-specific motifs conserved in OTUB subfamily of green plants enable rice OTUB1 to hydrolyse Met1 ubiquitin chains

Lu, L., Zhai, X., Li, X., Wang, S., Zhang, L., Wang, L., Jin, X., Liang, L., Deng, Z., Li, Z., Wang, Y., Fu, X., Hu, H., Wang, J., Mei, Z., He, Z., Wang, F.

(2022) Nat Commun 13: 4672

• DOI: https://doi.org/10.1038/s41467-022-32364-3

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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 114.16 kDa 
• Atom Count: 8,278 
• Modelled Residue Count: 966 
• Deposited Residue Count: 1,004 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin thioesterase	A, B, C, D	251	Oryza sativa Japonica Group	Mutation(s): 0  Gene Names: OsJ_28104 EC: 3.4.19.12
UniProt
Find proteins for B9G207 (Oryza sativa subsp. japonica) Explore B9G207  Go to UniProtKB:  B9G207

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.217 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.688	α = 90
b = 144.81	β = 90
c = 155.848	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-06-24 
Deposition Author(s): Lu, L.N., Liu, L., Wang, F.

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Funding Organization	Location	Grant Number
The National Key Research and Development Program of China	China	2017YFD0500400
The National Key Research and Development Program of China	China	2016YFC0906000
National Natural Science Foundation of China (NSFC)	China	32071269
National Natural Science Foundation of China (NSFC)	China	31770827
National Natural Science Foundation of China (NSFC)	China	21736002
National Natural Science Foundation of China (NSFC)	China	31640016
National Natural Science Foundation of China (NSFC)	China	31500980

Revision History  

• Version 1.0: 2020-06-24
  Type: Initial release
  
• Version 2.0: 2021-09-08
  Type: Coordinate replacement
  Reason: Real space R-factor
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2022-11-09
  Changes: Database references
• Version 2.2: 2023-11-29
  Changes: Data collection, Refinement description