6UUF | pdb_00006uuf

Crystal structure of a Nudix Hydrolase from M. Smegmatis, RenU

• PDB DOI: https://doi.org/10.2210/pdb6UUF/pdb

• Classification: HYDROLASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-10-30 Released: 2021-05-12 
• Deposition Author(s): Wright, K.M., Yoder, J., Shoemaker, S., Hernandez, A., Iheanacho, A., Marques, I., Amzel, M.L., Gabelli, S.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.231 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Structure of RenU

Wright, K.M., Yoder, J., Shoemaker, S., Hernandez, A., Iheanacho, A., Marques, I., Amzel, M.L., Nguyen, L., Gabelli, S.B.

To be published.

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: 35.73 kDa 
• Atom Count: 2,455 
• Modeled Residue Count: 316 
• Deposited Residue Count: 334 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nudix Hydrolase, RenU	A, B	167	Mycolicibacterium smegmatis MC2 155	Mutation(s): 3  Gene Names: mutT3, MSMEI_0773
UniProt
Find proteins for I7FED3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore I7FED3  Go to UniProtKB:  I7FED3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.231 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.198	α = 90
b = 118.738	β = 92.32
c = 36.432	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-05-12 
Deposition Author(s): Wright, K.M., Yoder, J., Shoemaker, S., Hernandez, A., Iheanacho, A., Marques, I., Amzel, M.L., Gabelli, S.B.

Revision History  

• Version 1.0: 2021-05-12
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description