7RAX

ATP-binding state of the nucleotide-binding domain of Hsp70 DnaK mutant T199A

• PDB DOI: https://doi.org/10.2210/pdb7RAX/pdb

• Classification: CHAPERONE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2021-07-04 Released: 2023-07-05 
• Deposition Author(s): Wang, W., Hendrickson, W.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.188 
• R-Value Work: 0.164 
• R-Value Observed: 0.164 

Literature

Visualization of Hsp70-catalyzed ATP Hydrolysis

Wang, W., Hendrickson, W.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 43.24 kDa 
• Atom Count: 3,491 
• Modelled Residue Count: 394 
• Deposited Residue Count: 394 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperone protein DnaK	A	393	Escherichia coli K-12	Mutation(s): 1  Gene Names: dnaK, FAZ83_07380
UniProt
Find proteins for P0A6Y8 (Escherichia coli (strain K12)) Explore P0A6Y8  Go to UniProtKB:  P0A6Y8

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	B [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	E [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.188 
• R-Value Work: 0.164 
• R-Value Observed: 0.164 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.806	α = 90
b = 48.118	β = 90.3
c = 63.951	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-05 
Deposition Author(s): Wang, W., Hendrickson, W.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM107462

Revision History  

• Version 1.0: 2023-07-05
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description