8PKQ | pdb_00008pkq

Crystal structure of PknD-34, a repeat fragment from the M. tuberculosis PknD beta-propeller

PDB DOI: https://doi.org/10.2210/pdb8PKQ/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2023-06-27 Released: 2024-07-10
Deposition Author(s): Wouters, S.M.L.
Funding Organization(s): Research Foundation - Flanders (FWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.213 (Depositor), 0.210 (DCC)
R-Value Work:
0.193 (Depositor), 0.190 (DCC)
R-Value Observed:
0.194 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Fragment-based assembly of a symmetric protein scaffold

Wouters, S.M.L., Noguchi, H., Voet, A.R.D.

To be published.

Macromolecule Content

Total Structure Weight: 27.3 kDa
Atom Count: 1,934
Modeled Residue Count: 242
Deposited Residue Count: 258
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
non-specific serine/threonine protein kinase	A, B, C	86	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: pknD_1, pknD_2, ERS007657_00042, ERS007663_00011, ERS007665_00696, ERS007720_00884, SAMEA2683035_02262 EC: 2.7.11.1
UniProt
Find proteins for P9WI79 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WI79 Go to UniProtKB: P9WI79
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WI79
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.213 (Depositor), 0.210 (DCC)
R-Value Work: 0.193 (Depositor), 0.190 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.351	α = 90
b = 95.351	β = 90
c = 69.829	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-10

Deposition Author(s):

Wouters, S.M.L.

Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	1S89918N
Research Foundation - Flanders (FWO)	Belgium	G0F9316N
Research Foundation - Flanders (FWO)	Belgium	G051917N

Revision History (Full details and data files)

Version 1.0: 2024-07-10
Type: Initial release

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.