4ICN | pdb_00004icn

Dihydrodipicolinate synthase from shewanella benthica

• PDB DOI: https://doi.org/10.2210/pdb4ICN/pdb

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


• Deposited: 2012-12-10 Released: 2013-12-11 
• Deposition Author(s): Wubben, J.M., Paxman, J.J., Dogovski, C., Parker, M.W., Perugini, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.250 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Cold enzymology offers insight into molecular evolution in quaternary structure

Wubben, J.M., Paxman, J.J., Dogovski, C., Parker, M.W., Perugini, M.A.

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: 63.91 kDa 
• Atom Count: 4,481 
• Modeled Residue Count: 595 
• Deposited Residue Count: 600 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIHYDRODIPICOLINATE SYNTHASE	A, B	300	Shewanella benthica	Mutation(s): 0  Gene Names: DAPA EC: 4.3.3.7
UniProt
Find proteins for A9DKW4 (Shewanella benthica KT99) Explore A9DKW4  Go to UniProtKB:  A9DKW4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4	F [auth A], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], E [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	G [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.250 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.09	α = 90
b = 84.03	β = 90
c = 143.72	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-11 
Deposition Author(s): Wubben, J.M., Paxman, J.J., Dogovski, C., Parker, M.W., Perugini, M.A.

Revision History  

• Version 1.0: 2013-12-11
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description