2IVB

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

PDB DOI: https://doi.org/10.2210/pdb2IVB/pdb

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

Deposited: 2006-06-09 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: 1.95 Å
R-Value Free: 0.207
R-Value Work: 0.145
R-Value Observed: 0.148

wwPDB Validation 3D Report Full Report

This is version 1.4 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: 172.62 kDa
Atom Count: 14,972
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 HYDRATASE	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 G] SDF format, chain CA [auth G] SDF format, chain GA [auth H] SDF format, chain IA [auth I] SDF format, chain JA [auth I] SDF format, chain K [auth A] SDF format, chain KA [auth I] SDF format, chain M [auth B] SDF format, chain NA [auth J] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain V [auth E] SDF format, chain X [auth F] SDF format, chain Y [auth F] MOL2 format, chain BA [auth G] MOL2 format, chain CA [auth G] MOL2 format, chain GA [auth H] MOL2 format, chain IA [auth I] MOL2 format, chain JA [auth I] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth I] MOL2 format, chain M [auth B] MOL2 format, chain NA [auth J] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain V [auth E] MOL2 format, chain X [auth F] MOL2 format, chain Y [auth F]	BA [auth G] CA [auth G] GA [auth H] IA [auth I] JA [auth I] BA [auth G], CA [auth G], GA [auth H], IA [auth I], JA [auth I], K [auth A], KA [auth I], M [auth B], NA [auth J], Q [auth D], R [auth D], S [auth D], T [auth D], V [auth E], X [auth F], Y [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth G] Focus chain CA [auth G] Focus chain GA [auth H] Focus chain IA [auth I] Focus chain JA [auth I] Focus chain K [auth A] Focus chain KA [auth I] Focus chain M [auth B] Focus chain NA [auth J] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Y [auth F]
AZI Query on AZI Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain FA [auth G] SDF format, chain P [auth C] SDF format, chain U [auth D] SDF format, chain W [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain P [auth C] MOL2 format, chain U [auth D] MOL2 format, chain W [auth E]	AA [auth F], FA [auth G], P [auth C], U [auth D], W [auth E]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain FA [auth G] Focus chain P [auth C] Focus chain U [auth D] Focus chain W [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain DA [auth G] SDF format, chain EA [auth G] SDF format, chain HA [auth H] SDF format, chain L [auth A] SDF format, chain LA [auth I] SDF format, chain MA [auth I] SDF format, chain N [auth B] SDF format, chain O [auth C] SDF format, chain OA [auth J] SDF format, chain Z [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain EA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth I] MOL2 format, chain MA [auth I] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain OA [auth J] MOL2 format, chain Z [auth F]	DA [auth G] EA [auth G] HA [auth H] L [auth A] LA [auth I] DA [auth G], EA [auth G], HA [auth H], L [auth A], LA [auth I], MA [auth I], N [auth B], O [auth C], OA [auth J], Z [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth G] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain L [auth A] Focus chain LA [auth I] Focus chain MA [auth I] Focus chain N [auth B] Focus chain O [auth C] Focus chain OA [auth J] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.207
R-Value Work: 0.145
R-Value Observed: 0.148
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.504	α = 69.86
b = 80.601	β = 71.38
c = 82.108	γ = 66.43

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 1.3: 2019-05-08
Changes: Data collection, Experimental preparation, Other
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Other, Refinement description