6HSA | pdb_00006hsa

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

• PDB DOI: https://doi.org/10.2210/pdb6HSA/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.
• Funding Organization(s): Engineering and Physical Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.92 Å
• R-Value Free: 
  0.120 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.101 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.102 (Depositor) 

Starting Model: experimental

Literature

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

Lapthorn, A.J., Ner, L., 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: 17.17 kDa 
• Atom Count: 1,571 
• Modeled Residue Count: 145 
• Deposited Residue Count: 145 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-dehydroquinate dehydratase	A	145	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ETE	B [auth A]	2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C9 H20 O5 ZNYRFEPBTVGZDN-UHFFFAOYSA-N
FLC	F [auth A]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
SER	C [auth A]	SERINE C3 H7 N O3 MTCFGRXMJLQNBG-REOHCLBHSA-N
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.92 Å
• R-Value Free:  0.120 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.101 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.102 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.476	α = 90
b = 79.476	β = 90
c = 72.033	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	EP/P00086X/1

Revision History  

• Version 1.0: 2019-10-23
  Type: Initial release
  
• Version 2.0: 2019-10-30
  Changes: Advisory, Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description