6OKZ | pdb_00006okz

Structure of VcINDY bound to Fumarate

• PDB DOI: https://doi.org/10.2210/pdb6OKZ/pdb

• Classification: membrane protein, transport protein
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2019-04-15 Released: 2020-10-28 
• Deposition Author(s): Sauer, D.B., Marden, J., Wang, D.N.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.29 Å
• R-Value Free: 
  0.286 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.247 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.248 (Depositor) 

Starting Model: experimental

Literature

Elevator mechanism dynamics in a sodium-coupled dicarboxylate transporter

Klinz-Thompson, C.D., Redondo, M.L., Mulligan, C., Sauer, D.B., Marden, J.J., Song, J., Tajkhorshid, E., Hunt, J.F., Stokes, D.L., Mindell, J.A., Wang, D.N., Gonzalez, R.L.

(2022) bioRxiv 

• DOI: https://doi.org/10.1101/2022.05.01.490196

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: 193.02 kDa 
• Atom Count: 13,120 
• Modelled Residue Count: 1,752 
• Deposited Residue Count: 1,796 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transporter, NadC family	A [auth C], B [auth D], C [auth A], D [auth B]	449	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: VC_A0025 Membrane Entity: Yes
UniProt
Find proteins for Q9KNE0 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KNE0  Go to UniProtKB:  Q9KNE0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FUM	G [auth C], M [auth B]	FUMARIC ACID C4 H4 O4 VZCYOOQTPOCHFL-OWOJBTEDSA-N
NA	E [auth C], F [auth C], H [auth D], I [auth D], J [auth A], K [auth A], L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.29 Å
• R-Value Free:  0.286 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.247 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.795	α = 90
b = 102.063	β = 98.94
c = 171.173	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-10-28 
Deposition Author(s): Sauer, D.B., Marden, J., Wang, D.N.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM121994
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01-NS108151

Revision History  

• Version 1.0: 2020-10-28
  Type: Initial release
  
• Version 1.1: 2022-05-18
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 2.0: 2023-11-15
  Changes: Advisory, Atomic model, Data collection