7DIB | pdb_00007dib

Crystal structure of D-threonine aldolase from Filomicrobium marinum

• PDB DOI: https://doi.org/10.2210/pdb7DIB/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Candidatus Filomicrobium marinum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-11-18 Released: 2021-08-04 
• Deposition Author(s): Seo, H., Kim, K.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Cbeta-Selective Aldol Addition of d-Threonine Aldolase by Spatial Constraint of Aldehyde Binding.

Park, S.-H., Seo, H., Seok, J., Kim, H., Kwon, K.K., Yeom, S.-J., Lee, S.-G., Kim, K.-J.

(2021) ACS Catal 11: 6892-6899

• DOI: https://doi.org/10.1021/acscatal.1c01348

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 84.99 kDa 
• Atom Count: 5,632 
• Modeled Residue Count: 740 
• Deposited Residue Count: 792 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-threonine aldolase	A, B	396	Candidatus Filomicrobium marinum	Mutation(s): 0  Gene Names: YBN1229_v1_3680 EC: 4.1.2.42
UniProt
Find proteins for A0A0D6JKM4 (Candidatus Filomicrobium marinum) Explore A0A0D6JKM4  Go to UniProtKB:  A0A0D6JKM4

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.965	α = 90
b = 178.051	β = 90
c = 65.458	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-08-04 
Deposition Author(s): Seo, H., Kim, K.-J.

Revision History  

• Version 1.0: 2021-08-04
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description