3EB2 | pdb_00003eb2

Crystal structure of Dihydrodipicolinate Synthase from Rhodopseudomonas palustris at 2.0A resolution

• PDB DOI: https://doi.org/10.2210/pdb3EB2/pdb

• Classification: LYASE
• Organism(s): Rhodopseudomonas palustris
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-26 Released: 2008-09-02 
• Deposition Author(s): Satyanarayana, L., Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.248 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.210 (DCC) 

Literature

Crystal structure of Dihydrodipicolinate Synthase from Rhodopseudomonas palustris at 2.0A resolution

Satyanarayana, L., Eswaramoorthy, S., Burley, S.K., Swaminathan, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 130.33 kDa 
• Atom Count: 9,399 
• Modeled Residue Count: 1,157 
• Deposited Residue Count: 1,200 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative dihydrodipicolinate synthetase	A, B, C, D	300	Rhodopseudomonas palustris	Mutation(s): 0  Gene Names: dapA1, RPA1571 EC: 4.2.1.52
UniProt
Find proteins for Q6N9H8 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6N9H8  Go to UniProtKB:  Q6N9H8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	E [auth A], F [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.248 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.210 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.746	α = 90
b = 120.852	β = 90
c = 135.076	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXCD	phasing
SHARP	phasing
CNS	refinement
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-02 
Deposition Author(s): Satyanarayana, L., Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-09-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references