28RZ | pdb_000028rz

Crystal Structure of the Apo Form of Mycobacterium tuberculosis Guanylate Kinase

PDB DOI: https://doi.org/10.2210/pdb28RZ/pdb

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

Deposited: 2026-02-16 Released: 2026-08-26
Deposition Author(s): Kozakiewicz-Piekarz, A., Grzegorska, M., Kurpiewska, K.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.280 (Depositor), 0.280 (DCC)
R-Value Work:
0.223 (Depositor), 0.223 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: experimental
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Literature

Crystal Structure of the Apo Form of Mycobacterium tuberculosis Guanylate Kinase

Kozakiewicz-Piekarz, A., Grzegorska, M., Kurpiewska, K.

To be published.

Macromolecule Content

Total Structure Weight: 20.3 kDa
Atom Count: 1,465
Modeled Residue Count: 186
Deposited Residue Count: 186
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanylate kinase	A	186	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: gmk, BQ2027_MB1424 EC: 2.7.4.8
UniProt
Find proteins for P0A5I5 (Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97)) Explore P0A5I5 Go to UniProtKB: P0A5I5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A5I5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	D [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.280 (Depositor), 0.280 (DCC)
R-Value Work: 0.223 (Depositor), 0.223 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.005	α = 90
b = 112.005	β = 90
c = 112.005	γ = 90

Software Package:

Software Name	Purpose
CrysalisPro	data collection
CrysalisPro	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-26

Deposition Author(s):

Kozakiewicz-Piekarz, A.

Funding Organization	Location	Grant Number
Not funded	Poland	--

Revision History (Full details and data files)

Version 1.0: 2026-08-26
Type: Initial release

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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.