3BB8 | pdb_00003bb8

E1 Dehydrase H220K Mutant

• PDB DOI: https://doi.org/10.2210/pdb3BB8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Yersinia pseudotuberculosis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-11-09 Released: 2008-09-16 
• Deposition Author(s): Tsai, S.-C., Smith, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.250 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

E1 Dehydrase H220K Mutant

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: 97.45 kDa 
• Atom Count: 6,594 
• Modeled Residue Count: 840 
• Deposited Residue Count: 874 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CDP-4-keto-6-deoxy-D-glucose-3-dehydrase	A, B	437	Yersinia pseudotuberculosis	Mutation(s): 1  Gene Names: ddhC 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
PLP	C [auth A], E [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
BEN	D [auth A], F [auth B]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.250 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.18	α = 90
b = 98.18	β = 90
c = 140.39	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
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-16 
Deposition Author(s): Tsai, S.-C., Smith, P.

Revision History  

• Version 1.0: 2008-09-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations