4RTF

Crystal structure of molecular chaperone DnaK from Mycobacterium tuberculosis H37Rv

• PDB DOI: https://doi.org/10.2210/pdb4RTF/pdb

• Classification: CHAPERONE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-11-14 Released: 2014-12-10 
• Deposition Author(s): Filippova, E.V., Minasov, G., Kiryukhina, O., Endres, M., Babnigg, G., Rubin, E., Sacchettini, J., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG), Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 0.269 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 

Starting Model: experimental

Literature

Crystal structure of molecular chaperone DnaK from Mycobacterium tuberculosis H37Rv

Filippova, E.V., Minasov, G., Kiryukhina, O., Endres, M., Babnigg, G., Rubin, E., Sacchettini, J., Joachimiak, A., Anderson, W.F.

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)

Macromolecule Content

• Total Structure Weight: 60.18 kDa 
• Atom Count: 2,650 
• Modelled Residue Count: 349 
• Deposited Residue Count: 546 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperone protein DnaK	A [auth D]	546	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: dnaK, P425_00363, RVBD_0350, WP_003401814

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	B [auth D]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
PG4	C [auth D]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 0.269 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 
• Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.866	α = 90
b = 117.866	β = 90
c = 134.943	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-10 
Deposition Author(s): Filippova, E.V., Minasov, G., Kiryukhina, O., Endres, M., Babnigg, G., Rubin, E., Sacchettini, J., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG), Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

Revision History  

• Version 1.0: 2014-12-10
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description