4PDV | pdb_00004pdv

Structure of K+ selective NaK mutant in barium and potassium

• PDB DOI: https://doi.org/10.2210/pdb4PDV/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Bacillus cereus ATCC 14579
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2014-04-22 Released: 2014-07-09 
• Deposition Author(s): Lam, Y., Zeng, W., Sauer, D.B., Jiang, Y.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Welch Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

High Resolution Structural Views of Rubidium, Cesium and Barium Binding within a Potassium Selective Channel Filter

Lam, Y., Zeng, W., Sauer, D.B., Jiang, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 22.66 kDa 
• Atom Count: 1,589 
• Modeled Residue Count: 189 
• Deposited Residue Count: 194 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Potassium channel protein	A, B	97	Bacillus cereus ATCC 14579	Mutation(s): 2  Gene Names: BC_0669 Membrane Entity: Yes
UniProt
Find proteins for Q81HW2 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)) Explore Q81HW2  Go to UniProtKB:  Q81HW2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BA	F [auth A], G [auth A], M [auth B]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N
MPD	H [auth A], I [auth A], N [auth B], O [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
K	C [auth A], D [auth A], E [auth A], J [auth B], K [auth B], L [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.065	α = 90
b = 68.065	β = 90
c = 89.614	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-07-09 
Deposition Author(s): Lam, Y., Zeng, W., Sauer, D.B., Jiang, Y.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM079179
Welch Foundation	United States	Grant I-1578

Revision History  

• Version 1.0: 2014-07-09
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
• Version 1.2: 2019-11-20
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description