2OCZ | pdb_00002ocz

The Structure of a Putative 3-Dehydroquinate Dehydratase from Streptococcus pyogenes.

• PDB DOI: https://doi.org/10.2210/pdb2OCZ/pdb

• Classification: LYASE
• Organism(s): Streptococcus pyogenes serotype M1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-12-21 Released: 2007-01-23 
• Deposition Author(s): Cuff, M.E., Duggan, E., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.230 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

The Structure of a Putative 3-Dehydroquinate Dehydratase from Streptococcus pyogenes.

Cuff, M.E., Duggan, E., Clancy, S., Joachimiak, A.

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.

Macromolecule Content 

• Total Structure Weight: 27.14 kDa 
• Atom Count: 2,132 
• Modeled Residue Count: 218 
• Deposited Residue Count: 231 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-dehydroquinate dehydratase	A	231	Streptococcus pyogenes serotype M1	Mutation(s): 10  Gene Names: aroD EC: 4.2.1.10
UniProt
Find proteins for P63590 (Streptococcus pyogenes serotype M1) Explore P63590  Go to UniProtKB:  P63590

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.230 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.688	α = 90
b = 81.688	β = 90
c = 85.364	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-23 
Deposition Author(s): Cuff, M.E., Duggan, E., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-01-23
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-11-13
  Changes: Structure summary