8PKR | pdb_00008pkr

Crystal structure of PknD-345, a repeat fragment from the M. tuberculosis PknD beta-propeller

PDB DOI: https://doi.org/10.2210/pdb8PKR/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: 0.95 Å
R-Value Free:
0.137 (Depositor), 0.137 (DCC)
R-Value Work:
0.128 (Depositor), 0.128 (DCC)
R-Value Observed:
0.128 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 8PKR

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

Literature

Computational design of the SAKe scaffold proteins

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

To be published.

Macromolecule Content

Total Structure Weight: 27.37 kDa
Atom Count: 2,214
Modeled Residue Count: 245
Deposited Residue Count: 256
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
non-specific serine/threonine protein kinase	A, B	128	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WI79
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 B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.95 Å
R-Value Free: 0.137 (Depositor), 0.137 (DCC)
R-Value Work: 0.128 (Depositor), 0.128 (DCC)
R-Value Observed: 0.128 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.701	α = 90
b = 83.241	β = 90
c = 83.453	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

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

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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.