2RFG | pdb_00002rfg

Crystal structure of dihydrodipicolinate synthase from Hahella chejuensis at 1.5A resolution

• PDB DOI: https://doi.org/10.2210/pdb2RFG/pdb

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


• Deposited: 2007-09-29 Released: 2007-10-23 
• Deposition Author(s): Kang, B.S., Kim, M.H., Kim, G.H., Kim, K.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.178 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of dihydrodipicolinate synthase from Hahella chejuensis at 1.5A resolution

Kang, B.S., Kim, M.H., Kim, G.H., Kim, K.J.

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: 129.41 kDa 
• Atom Count: 10,594 
• Modeled Residue Count: 1,164 
• Deposited Residue Count: 1,188 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A, B, C, D	297	Hahella chejuensis	Mutation(s): 0  EC: 4.2.1.52 (PDB Primary Data), 4.3.3.7 (UniProt)
UniProt
Find proteins for Q2S9K4 (Hahella chejuensis (strain KCTC 2396)) Explore Q2S9K4  Go to UniProtKB:  Q2S9K4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EOH	F [auth A]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.178 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.061	α = 90
b = 120.644	β = 90
c = 161.137	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-23 
Deposition Author(s): Kang, B.S., Kim, M.H., Kim, G.H., Kim, K.J.

Revision History  

• Version 1.0: 2007-10-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description