4OKI

X-ray structure of the nucleotide-binding subdomain of the enoylreductase domain of PpsC from Mycobacterium tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb4OKI/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-01-22 Released: 2015-08-05 
• Deposition Author(s): Faille, A., Mourey, L., Pedelacq, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.218 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

Insights into the catalytic mechanism of the DH domain of the Mycobacterium tuberculosis polyketide synthase PpsC and architecture of the beta-carbon processing domains

Faille, A., Slama, N., Quemard, A., Mourey, L., Pedelacq, J.D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 46.08 kDa 
• Atom Count: 3,033 
• Modelled Residue Count: 360 
• Deposited Residue Count: 432 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phthiocerol synthesis polyketide synthase type I PpsC	A, B	216	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: ppsC, Rv2933 EC: 2.3.1.41
UniProt
Find proteins for P96202 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P96202  Go to UniProtKB:  P96202

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
NA	C [auth A], E [auth A], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.218 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.885	α = 90
b = 78.743	β = 90
c = 88.796	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-05 
Deposition Author(s): Faille, A., Mourey, L., Pedelacq, J.D.

Revision History  

• Version 1.0: 2015-08-05
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations