3DZ1

Crystal structure of Dihydrodipicolinate Synthase from Rhodopseudomonas palustris at 1.87A resolution

• PDB DOI: https://doi.org/10.2210/pdb3DZ1/pdb

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


• Deposited: 2008-07-29 Released: 2008-08-12 
• 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: 1.87 Å
• R-Value Free: 0.215 
• R-Value Work: 0.190 
• R-Value Observed: 0.210 

Literature

Crystal structure of Dihydrodipicolinate Synthase from Rhodopseudomonas palustris at 1.87A 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: 34.76 kDa 
• Atom Count: 2,625 
• Modelled Residue Count: 301 
• Deposited Residue Count: 313 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A	313	Rhodopseudomonas palustris	Mutation(s): 0  Gene Names: RPA3190 EC: 4.2.1.52
UniProt
Find proteins for Q6N4Z3 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6N4Z3  Go to UniProtKB:  Q6N4Z3

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.215 
• R-Value Work: 0.190 
• R-Value Observed: 0.210 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.463	α = 90
b = 84.264	β = 90
c = 114.821	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: 2008-08-12 
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: 2008-08-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary