3BCX | pdb_00003bcx

E1 Dehydrase

• PDB DOI: https://doi.org/10.2210/pdb3BCX/pdb

• Classification: TRANSFERASE
• Organism(s): Yersinia pseudotuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-11-13 Released: 2007-11-27 
• Deposition Author(s): Tsai, S.-C., Smith, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.231 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

E1 Dehydrase.

Smith, P., Szu, P.-H., Tsai, S.-C., Liu, H.-W.

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)

Macromolecule Content 

• Total Structure Weight: 97.15 kDa 
• Atom Count: 6,771 
• Modeled Residue Count: 840 
• Deposited Residue Count: 874 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CDP-6-deoxy-L-threo-D-glycero-4-hexulose-3-dehydrase	A, B	437	Yersinia pseudotuberculosis	Mutation(s): 0  Gene Names: ascC EC: 2.6.1
UniProt
Find proteins for Q57323 (Yersinia pseudotuberculosis) Explore Q57323  Go to UniProtKB:  Q57323

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEN	D [auth A], E [auth A], F [auth B]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N
FE	C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.231 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.313	α = 90
b = 97.313	β = 90
c = 142.347	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-27 
Deposition Author(s): Tsai, S.-C., Smith, P.

Revision History  

• Version 1.0: 2007-11-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description