2IVG

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.

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYANATE LYASE	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00816
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain DB [auth J] SDF format, chain EB [auth J] SDF format, chain FA [auth F] SDF format, chain FB [auth J] SDF format, chain GA [auth F] SDF format, chain GB [auth J] SDF format, chain HA [auth F] SDF format, chain IA [auth F] SDF format, chain K [auth A] SDF format, chain LA [auth G] SDF format, chain M [auth B] SDF format, chain MA [auth G] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain PA [auth H] SDF format, chain QA [auth H] SDF format, chain RA [auth H] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain VA [auth I] SDF format, chain W [auth D] SDF format, chain WA [auth I] SDF format, chain X [auth D] SDF format, chain XA [auth I] SDF format, chain Y [auth D] SDF format, chain YA [auth I] SDF format, chain ZA [auth I] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain DB [auth J] MOL2 format, chain EB [auth J] MOL2 format, chain FA [auth F] MOL2 format, chain FB [auth J] MOL2 format, chain GA [auth F] MOL2 format, chain GB [auth J] MOL2 format, chain HA [auth F] MOL2 format, chain IA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth G] MOL2 format, chain M [auth B] MOL2 format, chain MA [auth G] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain PA [auth H] MOL2 format, chain QA [auth H] MOL2 format, chain RA [auth H] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain VA [auth I] MOL2 format, chain W [auth D] MOL2 format, chain WA [auth I] MOL2 format, chain X [auth D] MOL2 format, chain XA [auth I] MOL2 format, chain Y [auth D] MOL2 format, chain YA [auth I] MOL2 format, chain ZA [auth I]	BA [auth E] CA [auth E] DB [auth J] EB [auth J] FA [auth F] 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		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DB [auth J] Focus chain EB [auth J] Focus chain FA [auth F] Focus chain FB [auth J] Focus chain GA [auth F] Focus chain GB [auth J] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain K [auth A] Focus chain LA [auth G] Focus chain M [auth B] Focus chain MA [auth G] Focus chain O [auth C] Focus chain P [auth C] Focus chain PA [auth H] Focus chain QA [auth H] Focus chain RA [auth H] Focus chain U [auth D] Focus chain V [auth D] Focus chain VA [auth I] Focus chain W [auth D] Focus chain WA [auth I] Focus chain X [auth D] Focus chain XA [auth I] Focus chain Y [auth D] Focus chain YA [auth I] Focus chain ZA [auth I]
AZI Query on AZI Download Ideal Coordinates CCD File SDF format, chain R [auth C] MOL2 format, chain R [auth C]	R [auth C]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain R [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain AB [auth I] SDF format, chain BB [auth J] SDF format, chain CB [auth J] SDF format, chain DA [auth E] SDF format, chain EA [auth F] SDF format, chain HB [auth J] SDF format, chain JA [auth F] SDF format, chain KA [auth G] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain NA [auth G] SDF format, chain OA [auth H] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain SA [auth H] SDF format, chain T [auth D] SDF format, chain TA [auth I] SDF format, chain UA [auth I] SDF format, chain Z [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain AB [auth I] MOL2 format, chain BB [auth J] MOL2 format, chain CB [auth J] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain HB [auth J] MOL2 format, chain JA [auth F] MOL2 format, chain KA [auth G] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain NA [auth G] MOL2 format, chain OA [auth H] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain SA [auth H] MOL2 format, chain T [auth D] MOL2 format, chain TA [auth I] MOL2 format, chain UA [auth I] MOL2 format, chain Z [auth D]	AA [auth E] AB [auth I] BB [auth J] CB [auth J] DA [auth E] 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		Interactions Focus chain AA [auth E] Focus chain AB [auth I] Focus chain BB [auth J] Focus chain CB [auth J] Focus chain DA [auth E] Focus chain EA [auth F] Focus chain HB [auth J] Focus chain JA [auth F] Focus chain KA [auth G] Focus chain L [auth A] Focus chain N [auth B] Focus chain NA [auth G] Focus chain OA [auth H] Focus chain Q [auth C] Focus chain S [auth D] Focus chain SA [auth H] Focus chain T [auth D] Focus chain TA [auth I] Focus chain UA [auth I] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-10-28

Deposition Author(s):

Revision History (Full details and data files)

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