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.

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), 0.193 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

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

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| 3D Structure

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	3D Interactions
IBQ Query on IBQ Download:Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth C] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth C] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B], G [auth C]	IODO-BEDAQUILINE C₃₂ H₃₁ I N₂ O₂ UXPXAEJHNFTCFD-XLJNKUFUSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain G [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain G [auth C]
TAM Query on TAM Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	TRIS(HYDROXYETHYL)AMINOMETHANE C₇ H₁₇ N O₃ GKODZWOPPOTFGA-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

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), 0.193 (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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-01-20

Deposition Author(s):

Preiss, L.

Yildiz, O.

Meier, T.

Revision History (Full details and data files)

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