4XBK

2-deoxyribose-5-phosphate aldolase from Lactobacillus brevis

• PDB DOI: https://doi.org/10.2210/pdb4XBK/pdb

• Classification: LYASE
• Organism(s): Levilactobacillus brevis ATCC 14869 = DSM 20054
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-12-17 Released: 2015-11-04 
• Deposition Author(s): Jiao, X.-C., Pan, J., Xu, G.-C., Kong, X.-D., Chen, Q., Zhang, Z.-J., Xu, J.-H.
• Funding Organization(s): Ministry of Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.178 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 

Literature

Efficient synthesis of a statin precursor in high space-time yield by a new aldehyde-tolerant aldolase identified from Lactobacillus brevis

Jiao, X.-C., Pan, J., Xu, G.-C., Kong, X.-D., Chen, Q., Zhang, Z.-J., Xu, J.-H.

(2015) Catal Sci Technol 5: 4048-4054

• DOI: https://doi.org/10.1039/C5CY00537J

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: 56.28 kDa 
• Atom Count: 3,683 
• Modelled Residue Count: 434 
• Deposited Residue Count: 530 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyribose-phosphate aldolase	A, B	265	Levilactobacillus brevis ATCC 14869 = DSM 20054	Mutation(s): 0  Gene Names: deoC, HMPREF0495_01319 EC: 4.1.2.4
UniProt
Find proteins for U2PI02 (Levilactobacillus brevis ATCC 14869 = DSM 20054) Explore U2PI02  Go to UniProtKB:  U2PI02

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	C [auth B], D [auth B], E [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.178 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.882	α = 90
b = 96.882	β = 90
c = 119.593	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data processing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
HKL-2000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-11-04 
Deposition Author(s): Jiao, X.-C., Pan, J., Xu, G.-C., Kong, X.-D., Chen, Q., Zhang, Z.-J., Xu, J.-H.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology	China	No. 21276082

Revision History  

• Version 1.0: 2015-11-04
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations