3EIS | pdb_00003eis

Crystal Structure of Arylmalonate Decarboxylase

• PDB DOI: https://doi.org/10.2210/pdb3EIS/pdb

• Classification: LYASE
• Organism(s): Bordetella bronchiseptica
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-17 Released: 2009-09-22 
• Deposition Author(s): Nakasako, M., Obata, R., Miyamoto, K., Ohta, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

Structural Basis of the Enantioselective Decarboxylation by Arylmalonate Decarboxylase

Nakasako, M., Obata, R., Miyamoto, K., Ohta, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 100.48 kDa 
• Atom Count: 7,212 
• Modeled Residue Count: 931 
• Deposited Residue Count: 960 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arylmalonate decarboxylase	A, B, C, D	240	Bordetella bronchiseptica	Mutation(s): 0  EC: 4.1.1.76
UniProt
Find proteins for Q05115 (Bordetella bronchiseptica) Explore Q05115  Go to UniProtKB:  Q05115

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], H [auth B], J [auth C], K [auth C], L [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], G [auth A], I [auth B], M [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.508	α = 90
b = 99.395	β = 90
c = 139.981	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MLPHARE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-22 
Deposition Author(s): Nakasako, M., Obata, R., Miyamoto, K., Ohta, H.

Revision History  

• Version 1.0: 2009-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary