6NAY

Crystal structure of Neisseria meningitidis ClpP protease E31A+E58A activated double mutant

PDB DOI: https://doi.org/10.2210/pdb6NAY/pdb

Classification: HYDROLASE
Organism(s): Neisseria meningitidis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2018-12-06 Released: 2019-11-13
Deposition Author(s): Mabanglo, M.F., Houry, W.A.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.245
R-Value Work: 0.214
R-Value Observed: 0.214

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 680.25 kDa
Atom Count: 39,500
Modelled Residue Count: 4,905
Deposited Residue Count: 6,076
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit	A AA [auth a] B BA [auth b] C A, AA [auth a], B, BA [auth b], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	217	Neisseria meningitidis	Mutation(s): 2 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9JZ38
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.245
R-Value Work: 0.214
R-Value Observed: 0.214
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.707	α = 90.02
b = 119.84	β = 89.99
c = 127.861	γ = 90.02

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Currently 6NAY does not have a validation slider image.

Entry History & Funding Information

Deposition Data

Released Date: 2019-11-13

Deposition Author(s):

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 (Full details and data files)

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, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.