6I5T

Cryo-EM informed directed evolution of Nitrilase 4 leads to a change in quaternary structure.

PDB DOI: https://doi.org/10.2210/pdb6I5T/pdb
EM Map EMD-4418: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-11-14 Released: 2019-11-20
Deposition Author(s): Mulelu, A.E., Woodward, J.D.
Funding Organization(s): National Research Foundation in South Africa

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Cryo-EM informed directed evolution of nitrilase 4 leads to a change in quaternary structure.

Mulelu, A.E., Kirykowicz, A.M., Woodward, J.D.

To be published.

Macromolecule Content

Total Structure Weight: 238.6 kDa
Atom Count: 13,356
Modelled Residue Count: 1,734
Deposited Residue Count: 2,166
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional nitrilase/nitrile hydratase NIT4	A [auth F] B [auth E] C [auth D] D [auth C] E [auth B] A [auth F], B [auth E], C [auth D], D [auth C], E [auth B], F [auth A]	361	Arabidopsis thaliana	Mutation(s): 0 Gene Names: NIT4, At5g22300, MWD9.8 EC: 3.5.5.1 (PDB Primary Data), 3.5.5.4 (PDB Primary Data), 4.2.1.65 (PDB Primary Data)
UniProt
Find proteins for P46011 (Arabidopsis thaliana) Explore P46011 Go to UniProtKB: P46011
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P46011
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.14
RECONSTRUCTION	RELION	2.0

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-11-20

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation in South Africa	South Africa	Research Career Advancement Fellowship
	United Kingdom	Start: Synchrotron Techniques for African Research and Technology, ST/R002754/1

Revision History (Full details and data files)

Version 1.0: 2019-11-20
Type: Initial release
Version 1.1: 2019-12-18
Changes: Other
Version 1.2: 2024-05-15
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.