6KG3 | pdb_00006kg3

Crystal structure of Nicotinic acid mononucleotide adenylyltransferase mutant P22K/Y84V/Y118D/C132Q/W176F from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb6KG3/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli NCCP15648
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-07-10 Released: 2020-07-15 
• Deposition Author(s): Xue, S., Zhao, Z., Wang, X., Feng, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.08 Å
• R-Value Free: 
  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Nicotinic acid mononucleotide adenylyltransferase mutant P22K/Y84V/Y118D/C132Q/W176F from Escherichia coli

Xue, S., Feng, Y., Zhao, Z., Wang, X.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 146.76 kDa 
• Atom Count: 10,158 
• Modeled Residue Count: 1,257 
• Deposited Residue Count: 1,278 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable nicotinate-nucleotide adenylyltransferase	A, B, C, D, E, F	213	Escherichia coli NCCP15648	Mutation(s): 5  Gene Names: nadD, A610_610 EC: 2.7.7.18
UniProt
Find proteins for P0A752 (Escherichia coli (strain K12)) Explore P0A752  Go to UniProtKB:  P0A752

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.08 Å
• R-Value Free:  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.912	α = 90
b = 129.176	β = 103.177
c = 105.32	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-15 
Deposition Author(s): Xue, S., Zhao, Z., Wang, X., Feng, Y.

Revision History  

• Version 1.0: 2020-07-15
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description