4V1H | pdb_00004v1h

Crystal structure of a mycobacterial ATP synthase rotor ring in complex with Iodo-Bedaquiline

• PDB DOI: https://doi.org/10.2210/pdb4V1H/pdb

• Classification: HYDROLASE
• Organism(s): Mycolicibacterium phlei
• Mutation(s): No 


• Deposited: 2014-09-26 Released: 2016-01-20 
• Deposition Author(s): Preiss, L., Yildiz, O., Meier, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Structure of the Mycobacterial ATP Synthase Fo Rotor Ring in Complex with Iodo-Bedaquiline

Preiss, L., Langer, J.D., Yildiz, O., Koul, A., Meier, T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C9  (Explore in 3D)
Global Stoichiometry: Homo 9-mer - A9 

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

Macromolecule Content 

• Total Structure Weight: 27.81 kDa 
• Atom Count: 1,945 
• Modeled Residue Count: 255 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
F0F1 ATP SYNTHASE SUBUNIT C	A, B, C	86	Mycolicibacterium phlei	Mutation(s): 0  EC: 3.6.3.14

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IBQ	D [auth A], E [auth B], G [auth C]	IODO-BEDAQUILINE C32 H31 I N2 O2 UXPXAEJHNFTCFD-XLJNKUFUSA-N
TAM	F [auth B]	TRIS(HYDROXYETHYL)AMINOMETHANE C7 H17 N O3 GKODZWOPPOTFGA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.69	α = 90
b = 74.69	β = 90
c = 166.33	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Preiss, L., Yildiz, O., Meier, T.

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description