3I9X | pdb_00003i9x

Crystal structure of a mutT/nudix family protein from Listeria innocua

• PDB DOI: https://doi.org/10.2210/pdb3I9X/pdb

• Classification: HYDROLASE
• Organism(s): Listeria innocua
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-07-13 Released: 2009-07-28 
• Deposition Author(s): Bonanno, J.B., Gilmore, M., Bain, K.T., Miller, S., Romero, R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.276 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Literature

Crystal structure of a mutT/nudix family protein from Listeria innocua

Bonanno, J.B., Gilmore, M., Bain, K.T., Miller, S., Romero, R., Sauder, J.M., Burley, S.K., Almo, S.C.

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)

Macromolecule Content 

• Total Structure Weight: 21.02 kDa 
• Atom Count: 1,237 
• Modeled Residue Count: 157 
• Deposited Residue Count: 187 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mutT/nudix family protein	A	187	Listeria innocua	Mutation(s): 0  Gene Names: lin0490
UniProt
Find proteins for Q92EH0 (Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)) Explore Q92EH0  Go to UniProtKB:  Q92EH0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.276 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.129	α = 90
b = 96.129	β = 90
c = 97.594	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-28 
Deposition Author(s): Bonanno, J.B., Gilmore, M., Bain, K.T., Miller, S., Romero, R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references