6NAQ

Crystal structure of Neisseria meningitidis ClpP protease in Apo form

• PDB DOI: https://doi.org/10.2210/pdb6NAQ/pdb

• Classification: HYDROLASE
• Organism(s): Neisseria meningitidis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-12-06 Released: 2019-11-13 
• Deposition Author(s): Houry, W.A., Mabanglo, M.F., Pai, E.F., Eger, B.T., Bryson, S.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.246 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 

Literature

ClpP protease activation results from the reorganization of the electrostatic interaction networks at the entrance pores.

Mabanglo, M.F., Leung, E., Vahidi, S., Seraphim, T.V., Eger, B.T., Bryson, S., Bhandari, V., Zhou, J.L., Mao, Y.Q., Rizzolo, K., Barghash, M.M., Goodreid, J.D., Phanse, S., Babu, M., Barbosa, L.R.S., Ramos, C.H.I., Batey, R.A., Kay, L.E., Pai, E.F., Houry, W.A.

(2019) Commun Biol 2: 410-410

• DOI: https://doi.org/10.1038/s42003-019-0656-3

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 Evidence: SAXS

Macromolecule Content

• Total Structure Weight: 344.32 kDa 
• Atom Count: 20,681 
• Modelled Residue Count: 2,578 
• Deposited Residue Count: 3,052 
• 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	218	Neisseria meningitidis	Mutation(s): 0  Gene Names: clpP EC: 3.4.21.92
UniProt
Find proteins for Q9JZ38 (Neisseria meningitidis serogroup B (strain MC58)) Explore Q9JZ38  Go to UniProtKB:  Q9JZ38

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	AA [auth M], BA [auth N], O [auth A], P [auth B], Q [auth C], R [auth D], S [auth E], T [auth F], U [auth G], V [auth H], W [auth I], X [auth J], Y [auth K], Z [auth L]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.246 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.584	α = 90
b = 127.945	β = 90.19
c = 120.195	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Currently 6NAQ does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2019-11-13 
Deposition Author(s): Houry, W.A., Mabanglo, M.F., Pai, E.F., Eger, B.T., Bryson, S.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	XNE-86945
Canadian Institutes of Health Research (CIHR)	Canada	PJT-148564

Revision History  

• Version 1.0: 2019-11-13
  Type: Initial release
  
• Version 1.1: 2020-01-08
  Changes: Author supporting evidence
• Version 1.2: 2020-01-29
  Changes: Database references
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description