6NVA | pdb_00006nva

Crystal structure of Escherichia coli dihydrodipicolinate synthase and propionate covalently bound to K161.

• PDB DOI: https://doi.org/10.2210/pdb6NVA/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-02-04 Released: 2019-02-27 
• Deposition Author(s): Thomas, L.M., Chooback, L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 
  0.239 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.183 (Depositor) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Escherichia coli dihydrodipicolinate synthase and propionate covalently bound to K161.

Chooback, L., Thomas, L.M., Karsten, W., Sultana, F., Mesiya, S.

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)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 253.91 kDa 
• Atom Count: 20,204 
• Modeled Residue Count: 2,350 
• Deposited Residue Count: 2,352 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-tetrahydrodipicolinate synthase	A, B, C, D, E, F, G, H	294	Escherichia coli	Mutation(s): 1  Gene Names: dapA, A8C65_04230 EC: 4.3.3.7
UniProt
Find proteins for A0A066Q637 (Escherichia coli) Explore A0A066Q637  Go to UniProtKB:  A0A066Q637

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	I [auth A], J [auth B], K [auth C], M [auth E], N [auth F], P [auth G], Q [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	L [auth C], O [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free:  0.239 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.183 (Depositor) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.14	α = 109.72
b = 86.333	β = 104.24
c = 107.002	γ = 99.18

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-02-27 
Deposition Author(s): Thomas, L.M., Chooback, L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20GM103447

Revision History  

• Version 1.0: 2019-02-27
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations