6OXM

Crystal structure of L,L-diaminopimelate aminotransferase (DapL) from Verrucomicrobium spinosum

• PDB DOI: https://doi.org/10.2210/pdb6OXM/pdb

• Classification: TRANSFERASE
• Organism(s): Verrucomicrobium spinosum
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2019-05-13 Released: 2020-07-01 
• Deposition Author(s): Weatherhead, A., Meng, Y., Dobson, R., Hudson, A.
• Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.232 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Literature

Characterization of Diaminopimelate Aminotransferase from Verrucomicrobium Spinosum

Weatherhead, A.W., Meng, Y., Dobson, R., Hudson, 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)

Biological Assembly Evidence: SAXS

Macromolecule Content

• Total Structure Weight: 89.84 kDa 
• Atom Count: 6,675 
• Modelled Residue Count: 808 
• Deposited Residue Count: 822 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminopimelate aminotransferase	A, B	411	Verrucomicrobium spinosum	Mutation(s): 0  EC: 2.6.1.83

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.232 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.05	α = 90
b = 121.372	β = 102.01
c = 76.545	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-01 
Deposition Author(s): Weatherhead, A., Meng, Y., Dobson, R., Hudson, A.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB-1120541
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R15GM120653

Revision History  

• Version 1.0: 2020-07-01
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description