3IP8

Crystal structure of arylmalonate decarboxylase (AMDase) from Bordatella bronchiseptic in complex with benzylphosphonate

• PDB DOI: https://doi.org/10.2210/pdb3IP8/pdb

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


• Deposited: 2009-08-17 Released: 2009-10-06 
• Deposition Author(s): Okrasa, K., Levy, C., Leys, D., Micklefield, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.181 
• R-Value Work: 0.158 
• R-Value Observed: 0.159 

Literature

Structure-Guided Directed Evolution of Alkenyl and Arylmalonate Decarboxylases.

Okrasa, K., Levy, C., Wilding, M., Goodall, M., Baudendistel, N., Hauer, B., Leys, D., Micklefield, J.

(2009) Angew Chem Int Ed Engl 48: 7691-7694

• PubMed: 19739187 
• DOI: https://doi.org/10.1002/anie.200904112
• Primary Citation of Related Structures:  
  3IP8

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Organizational Affiliation: 

School of Chemistry, The University of Manchester, Manchester Interdisciplinary Biocentre, UK.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 26 kDa 
• Atom Count: 1,975 
• Modelled Residue Count: 232 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arylmalonate decarboxylase	A	248	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B85	B [auth A]	benzylphosphonic acid C7 H9 O3 P OGBVRMYSNSKIEF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
B85	PDBBind:  3IP8	Ki: 5.20e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.181 
• R-Value Work: 0.158 
• R-Value Observed: 0.159 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.64	α = 90
b = 65.6	β = 110.42
c = 41.88	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHENIX	model building
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-06 
Deposition Author(s): Okrasa, K., Levy, C., Leys, D., Micklefield, J.

Revision History  

• Version 1.0: 2009-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations