3DZB

Crystal structure of Prephenate dehydrogenase from Streptococcus thermophilus

• PDB DOI: https://doi.org/10.2210/pdb3DZB/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Streptococcus thermophilus LMG 18311
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-29 Released: 2008-08-12 
• Deposition Author(s): Zhang, Z., Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 0.278 
• R-Value Work: 0.234 
• R-Value Observed: 0.271 

Literature

Crystal structure of Prephenate dehydrogenase from Streptococcus thermophilus

Zhang, Z., Eswaramoorthy, S., Burley, S.K., Swaminathan, S.

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: 71.56 kDa 
• Atom Count: 4,499 
• Modelled Residue Count: 567 
• Deposited Residue Count: 634 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prephenate dehydrogenase	A, B	317	Streptococcus thermophilus LMG 18311	Mutation(s): 0  Gene Names: tyrA, stu0642 EC: 1.3.1.12
UniProt
Find proteins for Q5M554 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)) Explore Q5M554  Go to UniProtKB:  Q5M554

Small Molecules

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: 2.46 Å
• R-Value Free: 0.278 
• R-Value Work: 0.234 
• R-Value Observed: 0.271 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.906	α = 90
b = 145.005	β = 90
c = 56.227	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): Zhang, Z., 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: 2012-05-02
  Changes: Structure summary
• Version 1.3: 2017-10-25
  Changes: Refinement description
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-10-16
  Changes: Data collection, Database references, Structure summary