3B4U

Crystal structure of dihydrodipicolinate synthase from Agrobacterium tumefaciens str. C58

• PDB DOI: https://doi.org/10.2210/pdb3B4U/pdb

• Classification: LYASE
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-10-24 Released: 2007-12-04 
• Deposition Author(s): Zhang, R., Xu, L., Gu, J., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.156 
• R-Value Work: 0.127 
• R-Value Observed: 0.128 

Literature

The crystal structure of the dihydrodipicolinate synthase from Agrobacterium tumefaciens.

Zhang, R., Xu, L., Gu, J., Savchenko, A., Edwards, A.M., Joachimiak, 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: 62.6 kDa 
• Atom Count: 5,693 
• Modelled Residue Count: 575 
• Deposited Residue Count: 588 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A, B	294	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: dapA, AGR_C_4548, Atu2503
UniProt
Find proteins for A9CHR2 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CHR2  Go to UniProtKB:  A9CHR2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.156 
• R-Value Work: 0.127 
• R-Value Observed: 0.128 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.116	α = 79.35
b = 49.442	β = 89.06
c = 69.084	γ = 83.94

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-04 
Deposition Author(s): Zhang, R., Xu, L., Gu, J., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-12-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations