7KZU | pdb_00007kzu

Quasi-intermediate state (Q) of a truncated Hsp70 DnaK fused with a substrate peptide

• PDB DOI: https://doi.org/10.2210/pdb7KZU/pdb

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


• Deposited: 2020-12-10 Released: 2021-05-12 
• 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: 2.15 Å
• R-Value Free: 
  0.242 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Intermediates in allosteric equilibria of DnaK-ATP interactions with substrate peptides

Wang, W., Hendrickson, W.A.

(2021) Acta Crystallogr D Biol Crystallogr 77: 606-617

• DOI: https://doi.org/10.1107/S2059798321002436

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 60.48 kDa 
• Atom Count: 4,227 
• Modeled Residue Count: 532 
• Deposited Residue Count: 552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperone protein DnaK fused with substrate peptide,Chaperone protein DnaK fused with substrate peptide	A	552	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 4 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
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.242 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.135	α = 90
b = 145.135	β = 90
c = 122.212	γ = 120

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: 2021-05-12 
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: 2021-05-12
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description