1Z8F | pdb_00001z8f

Guanylate Kinase Double Mutant A58C, T157C from Mycobacterium tuberculosis (Rv1389)

PDB DOI: https://doi.org/10.2210/pdb1Z8F/pdb

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

Deposited: 2005-03-30 Released: 2005-04-12
Deposition Author(s): Chan, S., Sawaya, M.R., Choi, B., Zocchi, G., Perry, L.J., Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.236 (Depositor), 0.230 (DCC)
R-Value Work:
0.181 (Depositor), 0.180 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal Structure of Guanylate Kinase from Mycobacterium tuberculosis (Rv1389)

Chan, S., Sawaya, M.R., Choi, B., Zocchi, G., Perry, L.J.

To be published.

Macromolecule Content

Total Structure Weight: 24.41 kDa
Atom Count: 1,422
Modelled Residue Count: 184
Deposited Residue Count: 228
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanylate kinase	A	228	Mycobacterium tuberculosis	Mutation(s): 2 Gene Names: gmk EC: 2.7.4.8
UniProt
Find proteins for P9WKE9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WKE9 Go to UniProtKB: P9WKE9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WKE9
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMT Query on FMT 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]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.236 (Depositor), 0.230 (DCC)
R-Value Work: 0.181 (Depositor), 0.180 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.306	α = 90
b = 112.306	β = 90
c = 112.306	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-04-12

Deposition Author(s):

Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)

Revision History (Full details and data files)

Version 1.0: 2005-04-12
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2021-10-20
Changes: Database references, Derived calculations
Version 1.5: 2023-08-23
Changes: Data collection, Refinement description
Version 1.6: 2024-11-06
Changes: Structure summary

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.