6HS8 | pdb_00006hs8

The crystal structure of type II Dehydroquinase from Butyrivibrio crossotus DSM 2876

• PDB DOI: https://doi.org/10.2210/pdb6HS8/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Eshraghiella crossota DSM 2876
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-09-29 Released: 2019-10-23 
• Deposition Author(s): Lapthorn, A.J., Roszak, A.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.143 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of type II Dehydroquinase from Butyrivibrio crossotus DSM 2876

Lapthorn, A.J., Robertson, H., Roszak, A.W.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 16.97 kDa 
• Atom Count: 1,346 
• Modeled Residue Count: 144 
• Deposited Residue Count: 144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-dehydroquinate dehydratase	A	144	Eshraghiella crossota DSM 2876	Mutation(s): 0  Gene Names: aroQ, BUTYVIB_01550 EC: 4.2.1.10
UniProt
Find proteins for D4S0D1 (Eshraghiella crossota DSM 2876) Explore D4S0D1  Go to UniProtKB:  D4S0D1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	B [auth A], C [auth A], D [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.143 (Depositor) 

Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.33	α = 90
b = 125.33	β = 90
c = 125.33	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-23 
Deposition Author(s): Lapthorn, A.J., Roszak, A.W.

Revision History  

• Version 1.0: 2019-10-23
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description