3QWD

Crystal structure of ClpP from Staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb3QWD/pdb

• Classification: HYDROLASE
• Organism(s): Staphylococcus aureus subsp. aureus NCTC 8325
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-02-28 Released: 2011-05-18 
• Deposition Author(s): Geiger, S.R., Boettcher, T., Sieber, S.A., Cramer, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.226 
• R-Value Work: 0.208 
• R-Value Observed: 0.209 

Literature

A Conformational Switch Underlies ClpP Protease Function.

Geiger, S.R., Bottcher, T., Sieber, S.A., Cramer, P.

(2011) Angew Chem Int Ed Engl 50: 5749-5752

• PubMed: 21544912 
• DOI: https://doi.org/10.1002/anie.201100666
• Primary Citation of Related Structures:  
  3QWD

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Organizational Affiliation: 

Gene Center and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.

Biological Assembly 1  

Global Symmetry: Dihedral - D7  (Explore in 3D)
Global Stoichiometry: Homo 14-mer - A14 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C7  (Explore in 3D)
Global Stoichiometry: Homo 7-mer - A7 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C7  (Explore in 3D)
Global Stoichiometry: Homo 7-mer - A7 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 316.35 kDa 
• Atom Count: 20,404 
• Modelled Residue Count: 2,589 
• Deposited Residue Count: 2,842 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit	A, B, C, D, E, F, G, H, I, J, K, L, M, N	203	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0  Gene Names: clpP, SAOUHSC_00790 EC: 3.4.21.92
UniProt
Find proteins for Q2G036 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G036  Go to UniProtKB:  Q2G036

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	O [auth A], P [auth B], Q [auth C], R [auth D], S [auth L], T [auth L], U [auth M]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.226 
• R-Value Work: 0.208 
• R-Value Observed: 0.209 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 172.048	α = 90
b = 177.974	β = 90
c = 100.278	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
BUSTER	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-18 
Deposition Author(s): Geiger, S.R., Boettcher, T., Sieber, S.A., Cramer, P.

Revision History  

• Version 1.0: 2011-05-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations