5T26

Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase from Escherichia coli.

• PDB DOI: https://doi.org/10.2210/pdb5T26/pdb

• Classification: LYASE
• Organism(s): Escherichia coli IAI1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-08-23 Released: 2016-10-05 
• Deposition Author(s): Chooback, L., Thomas, L.M., Karsten, W.E., Fleming, C.D., Seabourn, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.207 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 

Starting Model: experimental

Literature

Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase from Escherichia coli.

Chooback, L., Thomas, L.M., Karsten, W.E., Fleming, C.D., Seabourn, P.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 63.79 kDa 
• Atom Count: 4,966 
• Modelled Residue Count: 587 
• Deposited Residue Count: 588 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-tetrahydrodipicolinate synthase	A, B	294	Escherichia coli IAI1	Mutation(s): 0  Gene Names: dapA, ECIAI1_2529 EC: 4.3.3.7
UniProt
Find proteins for P0A6L2 (Escherichia coli (strain K12)) Explore P0A6L2  Go to UniProtKB:  P0A6L2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	J [auth B]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
GOL	K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
74P	A, B	L-PEPTIDE LINKING	C11 H18 N2 O5		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.207 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.714	α = 90
b = 161.492	β = 90
c = 137.325	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-05 
Deposition Author(s): Chooback, L., Thomas, L.M., Karsten, W.E., Fleming, C.D., Seabourn, P.

Revision History  

• Version 1.0: 2016-10-05
  Type: Initial release
  
• Version 1.1: 2017-05-17
  Changes: Non-polymer description
• Version 1.2: 2017-08-23
  Changes: Data collection
• Version 1.3: 2018-05-30
  Changes: Data collection, Derived calculations
• Version 2.0: 2019-08-07
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Refinement description, Structure summary
• Version 2.1: 2019-10-02
  Changes: Data collection, Derived calculations
• Version 2.2: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.3: 2023-11-15
  Changes: Data collection, Derived calculations