6N2F | pdb_00006n2f

Meso-Diaminopimelate Decarboxylase from Arabidopsis thaliana (Isoform 2)

• PDB DOI: https://doi.org/10.2210/pdb6N2F/pdb

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


• Deposited: 2018-11-12 Released: 2019-04-24 
• Deposition Author(s): Crowther, J.M., Dobson, R.C.J.
• Funding Organization(s): Royal Society, National Science Foundation (NSF, United States)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.269 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Active site gating provides stereochemical control for meso-diaminopimelate decarboxylase

Crowther, J.M., Cross, P.J., Oliver, M.R., Leeman, M.M., Bartl, A.J., Weatherhead, A.W., North, R.A., Donovan, K.A., Kessans, S.A., Griffin, M.D.W., Suzuki, H., Hudson, A.O., Kassanmescheff, M., Dobson, R.C.J.

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 Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 94.3 kDa 
• Atom Count: 6,760 
• Modeled Residue Count: 834 
• Deposited Residue Count: 844 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminopimelate decarboxylase 2, chloroplastic	A, B	422	Arabidopsis thaliana	Mutation(s): 0  Gene Names: LYSA2, diDi 18A-1f, At5g11880, F14F18.50 EC: 4.1.1.20
UniProt
Find proteins for Q94A94 (Arabidopsis thaliana) Explore Q94A94  Go to UniProtKB:  Q94A94

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP (Subject of Investigation/LOI)	C [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
LYS (Subject of Investigation/LOI)	D [auth B]	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.269 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.381	α = 90
b = 107.989	β = 98.61
c = 80.929	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-04-24 
Deposition Author(s): Crowther, J.M., Dobson, R.C.J.

---

Funding Organization	Location	Grant Number
Royal Society	New Zealand	UOC1506
National Science Foundation (NSF, United States)	United States	MCB-1120541

Revision History  

• Version 1.0: 2019-04-24
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description