4D7Z | pdb_00004d7z

E. coli L-aspartate-alpha-decarboxylase mutant N72Q to a resolution of 1.9 Angstroms

• PDB DOI: https://doi.org/10.2210/pdb4D7Z/pdb

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


• Deposited: 2014-12-02 Released: 2016-01-13 
• Deposition Author(s): Bravo, J.P.K., Monteiro, D.C.F., Webb, M.E., Pearson, A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.244 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

The Structure of the E. Coli L-Aspartate-Alpha-Decarboxylase Mutant N72Q to a Resolution of 1.9 Angstroms

Bravo, J.P.K., Monteiro, D.C.F., Webb, M.E., Pearson, A.R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 15.34 kDa 
• Atom Count: 1,089 
• Modeled Residue Count: 123 
• Deposited Residue Count: 136 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ASPARTATE 1-DECARBOXYLASE BETA CHAIN	A	41	Escherichia coli	Mutation(s): 0  EC: 4.1.1.11
UniProt
Find proteins for P0A790 (Escherichia coli (strain K12)) Explore P0A790  Go to UniProtKB:  P0A790

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ASPARTATE 1-DECARBOXYLASE ALPHA CHAIN	B	95	Escherichia coli	Mutation(s): 1  EC: 4.1.1.11
UniProt
Find proteins for P0A790 (Escherichia coli (strain K12)) Explore P0A790  Go to UniProtKB:  P0A790

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	C [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SCN	D [auth B], E [auth B]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.244 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.35	α = 90
b = 71.35	β = 90
c = 112.31	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-13 
Deposition Author(s): Bravo, J.P.K., Monteiro, D.C.F., Webb, M.E., Pearson, A.R.

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations, Other
• Version 2.1: 2023-12-20
  Changes: Refinement description
• Version 2.2: 2024-11-13
  Changes: Structure summary