2IVQ | pdb_00002ivq

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

PDB DOI: https://doi.org/10.2210/pdb2IVQ/pdb

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

Deposited: 2006-06-14 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: 2.10 Å
R-Value Free:
0.243 (Depositor)
R-Value Work:
0.180 (Depositor)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
View more details

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: 173.16 kDa
Atom Count: 13,229
Modelled Residue Count: 1,560
Deposited Residue Count: 1,560
Unique protein chains: 1

Macromolecules

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(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 LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain BA [auth F] SDF format, chain CA [auth F] SDF format, chain FA [auth G] SDF format, chain GA [auth G] SDF format, chain HA [auth G] SDF format, chain K [auth A] SDF format, chain KA [auth H] SDF format, chain L [auth A] SDF format, chain LA [auth H] SDF format, chain MA [auth H] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain OA [auth I] SDF format, chain PA [auth I] SDF format, chain QA [auth I] SDF format, chain R [auth C] SDF format, chain SA [auth J] SDF format, chain T [auth D] SDF format, chain TA [auth J] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain X [auth E] SDF format, chain Y [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain GA [auth G] MOL2 format, chain HA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth H] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth H] MOL2 format, chain MA [auth H] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth I] MOL2 format, chain PA [auth I] MOL2 format, chain QA [auth I] MOL2 format, chain R [auth C] MOL2 format, chain SA [auth J] MOL2 format, chain T [auth D] MOL2 format, chain TA [auth J] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain BA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain FA [auth G] mmCIF format, chain GA [auth G] mmCIF format, chain HA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth H] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth H] mmCIF format, chain MA [auth H] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth I] mmCIF format, chain PA [auth I] mmCIF format, chain QA [auth I] mmCIF format, chain R [auth C] mmCIF format, chain SA [auth J] mmCIF format, chain T [auth D] mmCIF format, chain TA [auth J] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain X [auth E] mmCIF format, chain Y [auth E]	AA [auth F] BA [auth F] CA [auth F] FA [auth G] GA [auth G] AA [auth F], BA [auth F], CA [auth F], FA [auth G], GA [auth G], HA [auth G], K [auth A], KA [auth H], L [auth A], LA [auth H], MA [auth H], N [auth B], O [auth B], OA [auth I], PA [auth I], QA [auth I], R [auth C], SA [auth J], T [auth D], TA [auth J], U [auth D], V [auth D], X [auth E], Y [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain K [auth A] Focus chain KA [auth H] Focus chain L [auth A] Focus chain LA [auth H] Focus chain MA [auth H] Focus chain N [auth B] Focus chain O [auth B] Focus chain OA [auth I] Focus chain PA [auth I] Focus chain QA [auth I] Focus chain R [auth C] Focus chain SA [auth J] Focus chain T [auth D] Focus chain TA [auth J] Focus chain U [auth D] Focus chain V [auth D] Focus chain X [auth E] Focus chain Y [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain DA [auth F] SDF format, chain EA [auth F] SDF format, chain IA [auth G] SDF format, chain JA [auth H] SDF format, chain M [auth A] SDF format, chain NA [auth I] SDF format, chain P [auth B] SDF format, chain Q [auth C] SDF format, chain RA [auth J] SDF format, chain S [auth C] SDF format, chain UA [auth J] SDF format, chain W [auth D] SDF format, chain Z [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain JA [auth H] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth I] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain RA [auth J] MOL2 format, chain S [auth C] MOL2 format, chain UA [auth J] MOL2 format, chain W [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain IA [auth G] mmCIF format, chain JA [auth H] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth I] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain RA [auth J] mmCIF format, chain S [auth C] mmCIF format, chain UA [auth J] mmCIF format, chain W [auth D] mmCIF format, chain Z [auth E]	DA [auth F] EA [auth F] IA [auth G] JA [auth H] M [auth A] DA [auth F], EA [auth F], IA [auth G], JA [auth H], M [auth A], NA [auth I], P [auth B], Q [auth C], RA [auth J], S [auth C], UA [auth J], W [auth D], Z [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth F] Focus chain EA [auth F] Focus chain IA [auth G] Focus chain JA [auth H] Focus chain M [auth A] Focus chain NA [auth I] Focus chain P [auth B] Focus chain Q [auth C] Focus chain RA [auth J] Focus chain S [auth C] Focus chain UA [auth J] Focus chain W [auth D] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.243 (Depositor)
R-Value Work: 0.180 (Depositor)
R-Value Observed: 0.183 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.883	α = 69.99
b = 80.845	β = 71.98
c = 82.647	γ = 66.17

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