5AF3 | pdb_00005af3

X-RAY CRYSTAL STRUCTURE OF RV2018 FROM MYCOBACTERIUM TUBERCULOSIS

PDB DOI: https://doi.org/10.2210/pdb5AF3/pdb

Classification: DNA BINDING
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-01-18 Released: 2016-01-27
Deposition Author(s): Holton, S.J., Wilmanns, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.254 (Depositor), 0.253 (DCC)
R-Value Work:
0.210 (Depositor), 0.212 (DCC)
R-Value Observed:
0.213 (Depositor)

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

Literature

Crystal Structure and DNA Binding Ability of Myco Tuberculosis Vapbc49 Anti-Toxin Protein Bacterium

Holton, S.J., Pogenberg, V., Iborra, V., Wilmanns, M.

To be published.

Macromolecule Content

Total Structure Weight: 52.47 kDa
Atom Count: 3,599
Modeled Residue Count: 428
Deposited Residue Count: 482
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VAPBC49	A, B	241	Mycobacterium tuberculosis H37Rv	Mutation(s): 0
UniProt
Find proteins for O53464 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O53464 Go to UniProtKB: O53464
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O53464
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.254 (Depositor), 0.253 (DCC)
R-Value Work: 0.210 (Depositor), 0.212 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.935	α = 90
b = 81.935	β = 90
c = 75.361	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-01-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-01-27
Type: Initial release
Version 1.1: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other

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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.