6CV6

Crystal structure of 3-dehydroquinate dehydratase, type II, from Burkholderia phymatum STM815

• PDB DOI:  https://doi.org/10.2210/pdb6CV6/pdb

• Classification: LYASE
• Organism(s): Paraburkholderia phymatum STM815
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2018-03-27 Released: 2018-04-11 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.201 
• R-Value Work: 0.156 
• R-Value Observed: 0.157 

Literature

Crystal structure of 3-dehydroquinate dehydratase, type II, from Burkholderia phymatum STM815

Abendroth, J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 225.87 kDa 
• Atom Count: 14,369 
• Modelled Residue Count: 1,737 
• Deposited Residue Count: 1,992 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-dehydroquinate dehydratase	A, B, C, D, E, F, G, H, I, J, K, L	166	Paraburkholderia phymatum STM815	Mutation(s): 0  Gene Names: aroQ, Bphy_6025 EC: 4.2.1.10

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TAR	BA [auth E], EA [auth F], HA [auth G], KA [auth H], NA [auth I], O [auth A], QA [auth J], R [auth B], TA [auth K], V [auth C], WA [auth L], Y [auth D]	D(-)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-LWMBPPNESA-N
TLA	AA [auth E], CA [auth F], DA [auth F], FA [auth G], GA [auth G], IA [auth H], JA [auth H], LA [auth I], M [auth A], MA [auth I], N [auth A], OA [auth J], P [auth B], PA [auth J], Q [auth B], RA [auth K], SA [auth K], T [auth C], U [auth C], UA [auth L], VA [auth L], W [auth D], X [auth D], Z [auth E]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
CL	S [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.201 
• R-Value Work: 0.156 
• R-Value Observed: 0.157 
• Space Group: P 4₁ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M36CV6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.39	α = 90
b = 152.39	β = 90
c = 177.95	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-04-11 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2018-04-11
  Type: Initial release