4WIG

Crystal structure of E47D mutant cytidine deaminase from Mycobacterium tuberculosis (MtCDA E47D)

PDB DOI: https://doi.org/10.2210/pdb4WIG/pdb

Classification: HYDROLASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2014-09-25 Released: 2015-08-12
Deposition Author(s): Trivella, D.B.B., Sanchez-Quitian, A.Z., Basso, L.A., Santos, D.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.229
R-Value Work: 0.211
R-Value Observed: 0.212

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Functional and structural evidence for the catalytic role played by glutamate-47 residue in the mode of action of Mycobacterium tuberculosis cytidine deaminase

Sanchez-Quitian, Z.A., Rodrigues-Junior, E., Rehm, J.G., Eichler, P., Trivella, D.B.B., Bizarro, C.V., Basso, L.A., Santos, D.S.

(2015) RSC Adv 5: 830-840

DOI: https://doi.org/10.1039/C4RA13748E

Macromolecule Content

Total Structure Weight: 28.28 kDa
Atom Count: 2,150
Modelled Residue Count: 252
Deposited Residue Count: 266
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytidine deaminase	A, B	133	Mycobacterium tuberculosis	Mutation(s): 1 EC: 3.5.4.5
UniProt
Find proteins for P9WPH3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPH3 Go to UniProtKB: P9WPH3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WPH3
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.229
R-Value Work: 0.211
R-Value Observed: 0.212
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66	α = 90
b = 76.98	β = 90
c = 112.84	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-08-12

Deposition Author(s):

Trivella, D.B.B.

Sanchez-Quitian, A.Z.

Revision History (Full details and data files)

Version 1.0: 2015-08-12
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.