4CRY

Direct visualisation of strain-induced protein post-translational modification

• PDB DOI: https://doi.org/10.2210/pdb4CRY/pdb

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


• Deposited: 2014-03-02 Released: 2015-03-25 
• Deposition Author(s): Monteiro, D.C.F., Patel, V., Bartlett, C.P., Grant, T.D., Nozaki, S., Gowdy, J.A., Snell, E.H., Niki, H., Pearson, A.R., Webb, M.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.150 
• R-Value Work: 0.129 
• R-Value Observed: 0.130 

Starting Model: experimental

Literature

Direct Visualisation of Strain-Induced Protein Post-Translational Modification

Monteiro, D.C.F., Patel, V., Bartlett, C.P., Grant, T.D., Nozaki, S., Gowdy, J.A., Snell, E.H., Niki, H., Pearson, A.R., Webb, M.E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A4B4C4 

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

Macromolecule Content

• Total Structure Weight: 32.42 kDa 
• Atom Count: 2,271 
• Modelled Residue Count: 254 
• Deposited Residue Count: 280 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ASPARTATE 1-DECARBOXYLASE	A	41	Escherichia coli K-12	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
PANZ	B	137	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P37613 (Escherichia coli (strain K12)) Explore P37613  Go to UniProtKB:  P37613

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ASPARTATE 1-DECARBOXYLASE	C [auth G]	102	Escherichia coli K-12	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACO	D [auth B]	ACETYL COENZYME *A C23 H38 N7 O17 P3 S ZSLZBFCDCINBPY-ZSJPKINUSA-N
CL	F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	C [auth G]	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.150 
• R-Value Work: 0.129 
• R-Value Observed: 0.130 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.4	α = 90
b = 86.4	β = 90
c = 81	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-25 
Deposition Author(s): Monteiro, D.C.F., Patel, V., Bartlett, C.P., Grant, T.D., Nozaki, S., Gowdy, J.A., Snell, E.H., Niki, H., Pearson, A.R., Webb, M.E.

Revision History  

• Version 1.0: 2015-03-25
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary