6NAQ | pdb_00006naq

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free:
0.246 (Depositor), 0.246 (DCC)
R-Value Work:
0.207 (Depositor), 0.209 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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: 344.32 kDa
Atom Count: 20,681
Modeled Residue Count: 2,578
Deposited Residue Count: 3,052
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit	A, B, C, D, E 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 ATCC BAA-335 / MC58)) Explore Q9JZ38 Go to UniProtKB: Q9JZ38
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9JZ38
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K Query on K Download:Ideal Coordinates CCD File SDF format, chain AA [auth M] SDF format, chain S [auth E] SDF format, chain W [auth I] SDF format, chain Z [auth L] SDF format, chain Y [auth K] SDF format, chain X [auth J] SDF format, chain V [auth H] SDF format, chain U [auth G] SDF format, chain T [auth F] SDF format, chain R [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth B] SDF format, chain O [auth A] SDF format, chain BA [auth N] MOL2 format, chain AA [auth M] MOL2 format, chain S [auth E] MOL2 format, chain W [auth I] MOL2 format, chain Z [auth L] MOL2 format, chain Y [auth K] MOL2 format, chain X [auth J] MOL2 format, chain V [auth H] MOL2 format, chain U [auth G] MOL2 format, chain T [auth F] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth A] MOL2 format, chain BA [auth N] mmCIF format, chain AA [auth M] mmCIF format, chain S [auth E] mmCIF format, chain W [auth I] mmCIF format, chain Z [auth L] mmCIF format, chain Y [auth K] mmCIF format, chain X [auth J] mmCIF format, chain V [auth H] mmCIF format, chain U [auth G] mmCIF format, chain T [auth F] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth A] mmCIF format, chain BA [auth N]	AA [auth M] BA [auth N] O [auth A] P [auth B] Q [auth C] 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		Interactions Focus chain AA [auth M] Focus chain BA [auth N] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth H] Focus chain W [auth I] Focus chain X [auth J] Focus chain Y [auth K] Focus chain Z [auth L] Interactions & Density Focus chain AA [auth M] Focus chain BA [auth N] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth H] Focus chain W [auth I] Focus chain X [auth J] Focus chain Y [auth K] Focus chain Z [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.246 (Depositor), 0.246 (DCC)
R-Value Work: 0.207 (Depositor), 0.209 (DCC)
R-Value Observed: 0.209 (Depositor)

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

View Full Validation Report

View more in-depth experimental data

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, Derived calculations, Refinement description

6NAQ | pdb_00006naq

Crystal structure of Neisseria meningitidis ClpP protease in Apo form

Literature

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

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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