Biological Assembly 1  

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Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 135801.73 
• Atom Count: 8796 
• Residue Count: 1260 
• Unique protein chains: 1

3SI9

Crystal structure of Dihydrodipicolinate Synthase from Bartonella Henselae

• DOI: 10.2210/pdb3SI9/pdb

• Classification: LYASE
• Organism(s): Bartonella henselae (strain ATCC 49882 / DSM 28221 / Houston 1)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2011-06-17 Released: 2011-06-29 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID), Staker, B.L., Abendroth, J., Sankaran, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.233 
• R-Value Work: 0.183 

Literature

Cloning, expression, purification, crystallization and X-ray diffraction analysis of dihydrodipicolinate synthase from the human pathogenic bacterium Bartonella henselae strain Houston-1 at 2.1 angstrom resolution.

Naqvi, K.F., Staker, B.L., Dobson, R.C., Serbzhinskiy, D., Sankaran, B., Myler, P.J., Hudson, A.O.

(2016) Acta Crystallogr F Struct Biol Commun 72: 2-9

• PubMed: 26750477 
• DOI: 10.1107/S2053230X15023213


• PubMed Abstract: 
  

The enzyme dihydrodipicolinate synthase catalyzes the committed step in the synthesis of diaminopimelate and lysine to facilitate peptidoglycan and protein synthesis. Dihydrodipicolinate synthase catalyzes the condensation of L-aspartate 4-semialdehyde and pyruvate to synthesize L-2,3-dihydrodipicolinate. Here, the cloning, expression, purification, crystallization and X-ray diffraction analysis of dihydrodipicolinate synthase from the pathogenic bacterium Bartonella henselae, the causative bacterium of cat-scratch disease, are presented. Protein crystals were grown in conditions consisting of 20%(w/v) PEG 4000, 100 mM sodium citrate tribasic pH 5.5 and were shown to diffract to ∼2.10 Å resolution. They belonged to space group P212121, with unit-cell parameters a = 79.96, b = 106.33, c = 136.25 Å. The final R values were Rr.i.m. = 0.098, Rwork = 0.183, Rfree = 0.233.

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Organizational Affiliation: 

Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Dihydrodipicolinate synthase	A, B, C, D	315	Bartonella henselae (strain ATCC 49882 / DSM 28221 / Houston 1)	Mutation(s): 0  Gene Names: dapA EC: 4.3.3.7
Find proteins for Q6G468 (Bartonella henselae (strain ATCC 49882 / DSM 28221 / Houston 1)) Go to UniProtKB:  Q6G468

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EDO	A, B, C, D	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.233 
• R-Value Work: 0.183 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data DOI: 
  10.18430/M33SI9 Protein Diffraction

Unit Cell:

Length (Å)	Angle (°)
a = 79.963	α = 90.00
b = 106.334	β = 90.00
c = 136.253	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-06-17 
• Released Date: 2011-06-29 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID), Staker, B.L., Abendroth, J., Sankaran, B.

Revision History 

• Version 1.0: 2011-06-29
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2016-03-02
  Type: Database references