3LCW | pdb_00003lcw

L-KDO aldolase complexed with hydroxypyruvate

• PDB DOI: https://doi.org/10.2210/pdb3LCW/pdb

• Classification: LYASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-01-12 Released: 2011-01-19 
• Deposition Author(s): Chou, C.-Y., Wang, A.H.-J., Ko, T.-P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.274 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Model: experimental

Literature

Modulation of substrate specificities of D-sialic acid aldolase through single mutations of Val251

Chou, C.-Y., Ko, T.-P., Wu, K.-J., Huang, K.-F., Lin, C.-H., Wong, C.-H., Wang, A.H.-J.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 141.33 kDa 
• Atom Count: 9,473 
• Modeled Residue Count: 1,164 
• Deposited Residue Count: 1,276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylneuraminate lyase	A, B, C, D	319	Escherichia coli K-12	Mutation(s): 8  Gene Names: b3225, JW3194, nanA, npl EC: 4.1.3.3
UniProt
Find proteins for P0A6L4 (Escherichia coli (strain K12)) Explore P0A6L4  Go to UniProtKB:  P0A6L4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3PY	E [auth A], G [auth B], I [auth C], K [auth D]	3-HYDROXYPYRUVIC ACID C3 H4 O4 HHDDCCUIIUWNGJ-UHFFFAOYSA-N
SO4	F [auth A], H [auth B], J [auth C], L [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.274 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.828	α = 90
b = 120.828	β = 90
c = 195.879	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-19 
Deposition Author(s): Chou, C.-Y., Wang, A.H.-J., Ko, T.-P.

Revision History  

• Version 1.0: 2011-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Advisory, Refinement description
• Version 1.3: 2023-11-01
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary