6PI4 | pdb_00006pi4

Crystal structure of ATP synthase epsion chain ATP synthase epsilon chain (ATP synthase F1 sector epsilon subunit) (F-ATPase epsilon subunit) from Mycobacterium smegmatis

PDB DOI: https://doi.org/10.2210/pdb6PI4/pdb

Classification: PROTEIN TRANSPORT
Organism(s): Mycolicibacterium smegmatis MC2 155
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2019-06-25 Released: 2019-07-24
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.283 (Depositor), 0.280 (DCC)
R-Value Work:
0.220 (Depositor), 0.220 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of ATP synthase epsion chain ATP synthase epsilon chain (ATP synthase F1 sector epsilon subunit) (F-ATPase epsilon subunit) from Mycobacterium smegmatis

Abendroth, J., Dranow, D.M., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 14.45 kDa
Atom Count: 907
Modelled Residue Count: 119
Deposited Residue Count: 129
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase epsilon chain	A	129	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 Gene Names: atpC, MSMEG_4935, MSMEI_4808
UniProt
Find proteins for A0R1Z9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R1Z9 Go to UniProtKB: A0R1Z9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0R1Z9
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.283 (Depositor), 0.280 (DCC)
R-Value Work: 0.220 (Depositor), 0.220 (DCC)
R-Value Observed: 0.226 (Depositor)

Diffraction Data: https://doi.org/10.18430/m36pi4

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.87	α = 90
b = 75.32	β = 90
c = 71.02	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MR-Rosetta	phasing
Coot	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2019-07-24

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2019-07-24
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references
Version 1.2: 2024-04-03
Changes: Refinement description

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.