7DQE

Crystal structure of the ADP-bound mutant A(S23C)3B(N64C)3 complex from enterococcus hirae V-ATPase

• PDB DOI: https://doi.org/10.2210/pdb7DQE/pdb

• Classification: HYDROLASE
• Organism(s): Enterococcus hirae ATCC 9790
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-12-23 Released: 2021-12-29 
• Deposition Author(s): Maruyama, S., Nakamoto, K., Suzuki, K., Mizutani, K., Imai, F.L., Ishizuka-Katsura, Y., Shirouzu, M., Murata, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 0.253 
• R-Value Work: 0.226 
• R-Value Observed: 0.227 

Literature

The Combination of High-Speed AFM and X-ray Crystallography Reveals Rotary Catalytic Mechanism of Shaftless V1-ATPase

Imamura, M., Maruyama, S., Nakamoto, K., Kawai, F., Akiyama, T., Mizutani, K., Suzuki, K., Shirouzu, M., Iino, R., Uchihashi, T., Ando, T., Murata, T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 Pseudo Symmetry: Cyclic - C6  (Explore in 3D)
Pseudo Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 355.67 kDa 
• Atom Count: 24,093 
• Modelled Residue Count: 3,106 
• Deposited Residue Count: 3,195 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type sodium ATPase catalytic subunit A	A, B, C	600	Enterococcus hirae ATCC 9790	Mutation(s): 1  Gene Names: ntpA, EHR_08260 EC: 7.2.2.1
UniProt
Find proteins for Q08636 (Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258 / NCTC 12367 / WDCM 00089 / R)) Explore Q08636  Go to UniProtKB:  Q08636

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type sodium ATPase subunit B	D, E, F	465	Enterococcus hirae ATCC 9790	Mutation(s): 1  Gene Names: ntpB, EHR_08265
UniProt
Find proteins for Q08637 (Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258 / NCTC 12367 / WDCM 00089 / R)) Explore Q08637  Go to UniProtKB:  Q08637

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	H [auth A], K [auth B], M [auth C]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
SO4	I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	G [auth A], J [auth B], L [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 0.253 
• R-Value Work: 0.226 
• R-Value Observed: 0.227 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.03	α = 90
b = 121.09	β = 90
c = 231.47	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-12-29 
Deposition Author(s): Maruyama, S., Nakamoto, K., Suzuki, K., Mizutani, K., Imai, F.L., Ishizuka-Katsura, Y., Shirouzu, M., Murata, T.

Revision History  

• Version 1.0: 2021-12-29
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description