6WWD | pdb_00006wwd

Crystal structure of Nucleoside-triphosphatase / dITP/XTP pyrophosphatase from Mycobacterium abscessus ATCC 19977 / DSM 44196

PDB DOI: https://doi.org/10.2210/pdb6WWD/pdb

Classification: HYDROLASE
Organism(s): Mycobacteroides abscessus ATCC 19977
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2020-05-09 Released: 2020-05-20
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.244 (Depositor), 0.240 (DCC)
R-Value Work:
0.186 (Depositor), 0.190 (DCC)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Nucleoside-triphosphatase / dITP/XTP pyrophosphatase from Mycobacterium abscessus ATCC 19977 / DSM 44196

Abendroth, J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 90.81 kDa
Atom Count: 6,140
Modeled Residue Count: 776
Deposited Residue Count: 852
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dITP/XTP pyrophosphatase	A, B, C, D	213	Mycobacteroides abscessus ATCC 19977	Mutation(s): 0 Gene Names: MAB_1485 EC: 3.6.1.66
UniProt
Find proteins for B1MLZ4 (Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CCUG 20993 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543 / L948)) Explore B1MLZ4 Go to UniProtKB: B1MLZ4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B1MLZ4
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.244 (Depositor), 0.240 (DCC)
R-Value Work: 0.186 (Depositor), 0.190 (DCC)
R-Value Observed: 0.189 (Depositor)

Diffraction Data: https://doi.org/10.18430/m36wwd

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.69	α = 90
b = 104.04	β = 90
c = 146.5	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
SHELXDE	phasing
PHASER	phasing
ARP/wARP	model building
Coot	model building
PARROT	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2020-05-20

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2020-05-20
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references, Refinement description

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.