2R8W | pdb_00002r8w

The crystal structure of dihydrodipicolinate synthase (Atu0899) from Agrobacterium tumefaciens str. C58

• PDB DOI: https://doi.org/10.2210/pdb2R8W/pdb

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


• Deposited: 2007-09-11 Released: 2007-09-25 
• Deposition Author(s): Tan, K., Dong, A., Xu, X., Gu, J., Zheng, H., Edwards, A.M., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.184 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Literature

The crystal structure of dihydrodipicolinate synthase (Atu0899) from Agrobacterium tumefaciens str. C58.

Tan, K., Dong, A., Xu, X., Gu, J., Zheng, H., Edwards, A.M., Savchenko, A., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 72.47 kDa 
• Atom Count: 5,187 
• Modeled Residue Count: 596 
• Deposited Residue Count: 664 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AGR_C_1641p	A, B	332	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: AGR_C_1641
UniProt
Find proteins for Q7D0E8 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7D0E8  Go to UniProtKB:  Q7D0E8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A], F [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.184 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.994	α = 90
b = 95.994	β = 90
c = 103.12	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-25 
Deposition Author(s): Tan, K., Dong, A., Xu, X., Gu, J., Zheng, H., Edwards, A.M., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-09-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary