6VH5

Crystal structure of prephenate dehydratase from brucella melitensis biovar abortus 2308 in complex with phenylalanine

• PDB DOI: https://doi.org/10.2210/pdb6VH5/pdb

• Classification: HYDROLASE
• Organism(s): Brucella abortus 2308
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2020-01-09 Released: 2020-01-29 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.251 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 

Starting Models: experimental

Literature

Crystal structure of prephenate dehydratase from Brucella melitensis biovar abortus 2308 in complex with phenylalanine

Abendroth, J., Dranow, D.M., Lorimer, D.D., Bullen, J.C., Sankaran, B., Horanyi, P.S., Edwards, T.E.

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 137.56 kDa 
• Atom Count: 8,683 
• Modelled Residue Count: 1,122 
• Deposited Residue Count: 1,232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prephenate dehydratase:Amino acid-binding ACT	A, B, C, D	308	Brucella abortus 2308	Mutation(s): 0  Gene Names: pheA, BAB1_0034 EC: 4.2.1.51
UniProt
Find proteins for Q2YPM5 (Brucella abortus (strain 2308)) Explore Q2YPM5  Go to UniProtKB:  Q2YPM5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PHE	E [auth A], G [auth B], J [auth C], L [auth D]	PHENYLALANINE C9 H11 N O2 COLNVLDHVKWLRT-QMMMGPOBSA-N
EDO	F [auth A], H [auth B], I [auth B], K [auth C], M [auth D], N [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.251 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.18430/m36vh5

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 226.95	α = 90
b = 61.25	β = 112.95
c = 120.05	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
MR-Rosetta	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-01-29 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2020-01-29
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-04-03
  Changes: Refinement description