5CCA | pdb_00005cca

Crystal structure of Mtb toxin

PDB DOI: https://doi.org/10.2210/pdb5CCA/pdb

Classification: HYDROLASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-07-01 Released: 2016-09-07
Deposition Author(s): Cascio, D., Arbing, M., de Serrano, V., Eisenberg, D., Miallau, L., TB Structural Genomics Consortium (TBSGC)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.302 (Depositor), 0.310 (DCC)
R-Value Work:
0.300 (Depositor), 0.305 (DCC)
R-Value Observed:
0.300 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5CCA

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of Mtb toxin

Cascio, D., Arbing, M., de Serrano, V., Eisenberg, D., Miallau, L., TB Structural Genomics Consortium (TBSGC)

To be published.

Macromolecule Content

Total Structure Weight: 27.03 kDa
Atom Count: 1,379
Modeled Residue Count: 185
Deposited Residue Count: 248
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoribonuclease MazF3	A, B	124	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: mazF3, MT1134 EC: 3.1
UniProt
Find proteins for P9WIH9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WIH9 Go to UniProtKB: P9WIH9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WIH9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.302 (Depositor), 0.310 (DCC)
R-Value Work: 0.300 (Depositor), 0.305 (DCC)
R-Value Observed: 0.300 (Depositor)

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.555	α = 90
b = 105.555	β = 90
c = 142.417	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
REFMAC	refinement
HKL-2000	data reduction
MR-Rosetta	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-09-07

Deposition Author(s):

TB Structural Genomics Consortium (TBSGC)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	99-S150606
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	PO1AIO68135

Revision History (Full details and data files)

Version 1.0: 2016-09-07
Type: Initial release
Version 1.1: 2017-09-27
Changes: Advisory, Author supporting evidence, Derived calculations, Refinement description
Version 1.2: 2019-12-04
Changes: Author supporting evidence
Version 1.3: 2023-09-27
Changes: Advisory, Data collection, Database references, Refinement description
Version 1.4: 2024-10-09
Changes: Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.