2IVG | pdb_00002ivg

SITE DIRECTED MUTAGENESIS OF KEY RESIDUES INVOLVED IN THE CATALYTIC MECHANISM OF CYANASE

• PDB DOI: https://doi.org/10.2210/pdb2IVG/pdb

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


• Deposited: 2006-06-13 Released: 2008-10-28 
• Deposition Author(s): Guilloton, M., Walsh, M.A., Joachimiak, A., Anderson, P.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.188 (Depositor) 
• R-Value Work: 
  0.145 (Depositor) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

Literature

A Twin Set of Low Pka Arginines Ensures the Concerted Acid Base Catalytic Mechanism of Cyanase

Guilloton, M., Walsh, M.A., Joachimiak, A., Anderson, P.M.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D5  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

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

Macromolecule Content

• Total Structure Weight: 173.65 kDa 
• Atom Count: 13,926 
• Modelled Residue Count: 1,560 
• Deposited Residue Count: 1,560 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYANATE LYASE	A, B, C, D, E, F, G, H, I, J	156	Escherichia coli	Mutation(s): 1  EC: 4.2.1.104
UniProt
Find proteins for P00816 (Escherichia coli (strain K12)) Explore P00816  Go to UniProtKB:  P00816

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	BA [auth E], CA [auth E], DB [auth J], EB [auth J], FA [auth F], FB [auth J], GA [auth F], GB [auth J], HA [auth F], IA [auth F], K [auth A], LA [auth G], M [auth B], MA [auth G], O [auth C], P [auth C], PA [auth H], QA [auth H], RA [auth H], U [auth D], V [auth D], VA [auth I], W [auth D], WA [auth I], X [auth D], XA [auth I], Y [auth D], YA [auth I], ZA [auth I]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
AZI	R [auth C]	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N
CL	AA [auth E], AB [auth I], BB [auth J], CB [auth J], DA [auth E], EA [auth F], HB [auth J], JA [auth F], KA [auth G], L [auth A], N [auth B], NA [auth G], OA [auth H], Q [auth C], S [auth D], SA [auth H], T [auth D], TA [auth I], UA [auth I], Z [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.188 (Depositor) 
• R-Value Work:  0.145 (Depositor) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.392	α = 70.69
b = 80.897	β = 75.98
c = 81.094	γ = 65.15

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-28 
Deposition Author(s): Guilloton, M., Walsh, M.A., Joachimiak, A., Anderson, P.M.

Revision History  

• Version 1.0: 2008-10-28
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2018-12-19
  Changes: Advisory, Atomic model, Data collection, Derived calculations
• Version 2.1: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 2.2: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description