5G1S | pdb_00005g1s

Open conformation of Francisella tularensis ClpP at 1.7 A

PDB DOI: https://doi.org/10.2210/pdb5G1S/pdb

Classification: HYDROLASE
Organism(s): Francisella tularensis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-03-30 Released: 2016-10-19
Deposition Author(s): Diaz-Saez, L., Pankov, G., Hunter, W.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.242 (Depositor), 0.246 (DCC)
R-Value Work:
0.204 (Depositor), 0.212 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: other
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Open and compressed conformations of Francisella tularensis ClpP.

Diaz-Saez, L., Pankov, G., Hunter, W.N.

(2017) Proteins 85: 188-194

PubMed: 27802578 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/prot.25197
Primary Citation Related Structures:
5G1Q, 5G1R, 5G1S

PubMed Abstract:
Caseinolytic proteases are large oligomeric assemblies responsible for maintaining protein homeostasis in bacteria and in so doing influence a wide range of biological processes. The functional assembly involves three chaperones together with the oligomeric caseinolytic protease catalytic subunit P (ClpP). This protease represents a potential target for therapeutic intervention in pathogenic bacteria. Here, we detail an efficient protocol for production of recombinant ClpP from Francisella tularensis, and the structural characterization of three crystal forms which grow under similar conditions. One crystal form reveals a compressed state of the ClpP tetradecamer and two forms an open state. A comparison of the two types of structure infers that differences at the enzyme active site result from a conformational change involving a highly localized disorder-order transition of a β-strand α-helix combination. This transition occurs at a subunit-subunit interface. Our study may now underpin future efforts in a structure-based approach to target ClpP for inhibitor or activator development. Proteins 2016; 85:188-194. © 2016 Wiley Periodicals, Inc.

Organizational Affiliation

Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom.

Macromolecule Content

Total Structure Weight: 470.75 kDa
Atom Count: 37,499
Modeled Residue Count: 3,966
Deposited Residue Count: 4,221
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, O, P, Q, R, S, T, U	201	Francisella tularensis	Mutation(s): 0 Gene Names: clpP, DR86_1343 EC: 3.4.21.92
UniProt
Find proteins for Q5NH47 (Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)) Explore Q5NH47 Go to UniProtKB: Q5NH47
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5NH47
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MRD Query on MRD Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain EA [auth D] SDF format, chain HB [auth P] SDF format, chain JB [auth Q] SDF format, chain KA [auth G] SDF format, chain NB [auth S] SDF format, chain PA [auth I] SDF format, chain QB [auth T] SDF format, chain TB [auth U] SDF format, chain UA [auth K] SDF format, chain V [auth A] SDF format, chain VA [auth K] SDF format, chain XA [auth L] SDF format, chain TA [auth K] SDF format, chain RB [auth T] SDF format, chain FB [auth O] SDF format, chain DB [auth N] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain HB [auth P] MOL2 format, chain JB [auth Q] MOL2 format, chain KA [auth G] MOL2 format, chain NB [auth S] MOL2 format, chain PA [auth I] MOL2 format, chain QB [auth T] MOL2 format, chain TB [auth U] MOL2 format, chain UA [auth K] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth K] MOL2 format, chain XA [auth L] MOL2 format, chain TA [auth K] MOL2 format, chain RB [auth T] MOL2 format, chain FB [auth O] MOL2 format, chain DB [auth N] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain HB [auth P] mmCIF format, chain JB [auth Q] mmCIF format, chain KA [auth G] mmCIF format, chain NB [auth S] mmCIF format, chain PA [auth I] mmCIF format, chain QB [auth T] mmCIF format, chain TB [auth U] mmCIF format, chain UA [auth K] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth K] mmCIF format, chain XA [auth L] mmCIF format, chain TA [auth K] mmCIF format, chain RB [auth T] mmCIF format, chain FB [auth O] mmCIF format, chain DB [auth N]	AA [auth C] BA [auth C] DB [auth N] EA [auth D] FB [auth O] AA [auth C], BA [auth C], DB [auth N], EA [auth D], FB [auth O], HB [auth P], JB [auth Q], KA [auth G], NB [auth S], PA [auth I], QB [auth T], RB [auth T], TA [auth K], TB [auth U], UA [auth K], V [auth A], VA [auth K], XA [auth L]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain DB [auth N] Focus chain EA [auth D] Focus chain FB [auth O] Focus chain HB [auth P] Focus chain JB [auth Q] Focus chain KA [auth G] Focus chain NB [auth S] Focus chain PA [auth I] Focus chain QB [auth T] Focus chain RB [auth T] Focus chain TA [auth K] Focus chain TB [auth U] Focus chain UA [auth K] Focus chain V [auth A] Focus chain VA [auth K] Focus chain XA [auth L] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain DB [auth N] Focus chain EA [auth D] Focus chain FB [auth O] Focus chain HB [auth P] Focus chain JB [auth Q] Focus chain KA [auth G] Focus chain NB [auth S] Focus chain PA [auth I] Focus chain QB [auth T] Focus chain RB [auth T] Focus chain TA [auth K] Focus chain TB [auth U] Focus chain UA [auth K] Focus chain V [auth A] Focus chain VA [auth K] Focus chain XA [auth L]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain AB [auth M] SDF format, chain CB [auth N] SDF format, chain FA [auth E] SDF format, chain LA [auth G] SDF format, chain MB [auth S] SDF format, chain OA [auth I] SDF format, chain RA [auth J] SDF format, chain UB [auth U] SDF format, chain YA [auth L] SDF format, chain Z [auth C] SDF format, chain X [auth B] SDF format, chain PB [auth T] SDF format, chain IA [auth F] SDF format, chain HA [auth F] MOL2 format, chain AB [auth M] MOL2 format, chain CB [auth N] MOL2 format, chain FA [auth E] MOL2 format, chain LA [auth G] MOL2 format, chain MB [auth S] MOL2 format, chain OA [auth I] MOL2 format, chain RA [auth J] MOL2 format, chain UB [auth U] MOL2 format, chain YA [auth L] MOL2 format, chain Z [auth C] MOL2 format, chain X [auth B] MOL2 format, chain PB [auth T] MOL2 format, chain IA [auth F] MOL2 format, chain HA [auth F] mmCIF format, chain AB [auth M] mmCIF format, chain CB [auth N] mmCIF format, chain FA [auth E] mmCIF format, chain LA [auth G] mmCIF format, chain MB [auth S] mmCIF format, chain OA [auth I] mmCIF format, chain RA [auth J] mmCIF format, chain UB [auth U] mmCIF format, chain YA [auth L] mmCIF format, chain Z [auth C] mmCIF format, chain X [auth B] mmCIF format, chain PB [auth T] mmCIF format, chain IA [auth F] mmCIF format, chain HA [auth F]	AB [auth M] CB [auth N] FA [auth E] HA [auth F] IA [auth F] AB [auth M], CB [auth N], FA [auth E], HA [auth F], IA [auth F], LA [auth G], MB [auth S], OA [auth I], PB [auth T], RA [auth J], UB [auth U], X [auth B], YA [auth L], Z [auth C]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain AB [auth M] Focus chain CB [auth N] Focus chain FA [auth E] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain LA [auth G] Focus chain MB [auth S] Focus chain OA [auth I] Focus chain PB [auth T] Focus chain RA [auth J] Focus chain UB [auth U] Focus chain X [auth B] Focus chain YA [auth L] Focus chain Z [auth C] Interactions & Density Focus chain AB [auth M] Focus chain CB [auth N] Focus chain FA [auth E] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain LA [auth G] Focus chain MB [auth S] Focus chain OA [auth I] Focus chain PB [auth T] Focus chain RA [auth J] Focus chain UB [auth U] Focus chain X [auth B] Focus chain YA [auth L] Focus chain Z [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain BB [auth M] SDF format, chain CA [auth C] SDF format, chain DA [auth D] SDF format, chain EB [auth N] SDF format, chain GA [auth E] SDF format, chain IB [auth P] SDF format, chain KB [auth Q] SDF format, chain MA [auth G] SDF format, chain QA [auth I] SDF format, chain SA [auth J] SDF format, chain SB [auth T] SDF format, chain W [auth A] SDF format, chain WA [auth K] SDF format, chain ZA [auth L] SDF format, chain Y [auth B] SDF format, chain VB [auth U] SDF format, chain OB [auth S] SDF format, chain NA [auth H] SDF format, chain LB [auth R] SDF format, chain JA [auth F] SDF format, chain GB [auth O] MOL2 format, chain BB [auth M] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain EB [auth N] MOL2 format, chain GA [auth E] MOL2 format, chain IB [auth P] MOL2 format, chain KB [auth Q] MOL2 format, chain MA [auth G] MOL2 format, chain QA [auth I] MOL2 format, chain SA [auth J] MOL2 format, chain SB [auth T] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth K] MOL2 format, chain ZA [auth L] MOL2 format, chain Y [auth B] MOL2 format, chain VB [auth U] MOL2 format, chain OB [auth S] MOL2 format, chain NA [auth H] MOL2 format, chain LB [auth R] MOL2 format, chain JA [auth F] MOL2 format, chain GB [auth O] mmCIF format, chain BB [auth M] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain EB [auth N] mmCIF format, chain GA [auth E] mmCIF format, chain IB [auth P] mmCIF format, chain KB [auth Q] mmCIF format, chain MA [auth G] mmCIF format, chain QA [auth I] mmCIF format, chain SA [auth J] mmCIF format, chain SB [auth T] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth K] mmCIF format, chain ZA [auth L] mmCIF format, chain Y [auth B] mmCIF format, chain VB [auth U] mmCIF format, chain OB [auth S] mmCIF format, chain NA [auth H] mmCIF format, chain LB [auth R] mmCIF format, chain JA [auth F] mmCIF format, chain GB [auth O]	BB [auth M] CA [auth C] DA [auth D] EB [auth N] GA [auth E] BB [auth M], CA [auth C], DA [auth D], EB [auth N], GA [auth E], GB [auth O], IB [auth P], JA [auth F], KB [auth Q], LB [auth R], MA [auth G], NA [auth H], OB [auth S], QA [auth I], SA [auth J], SB [auth T], VB [auth U], W [auth A], WA [auth K], Y [auth B], ZA [auth L]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain BB [auth M] Focus chain CA [auth C] Focus chain DA [auth D] Focus chain EB [auth N] Focus chain GA [auth E] Focus chain GB [auth O] Focus chain IB [auth P] Focus chain JA [auth F] Focus chain KB [auth Q] Focus chain LB [auth R] Focus chain MA [auth G] Focus chain NA [auth H] Focus chain OB [auth S] Focus chain QA [auth I] Focus chain SA [auth J] Focus chain SB [auth T] Focus chain VB [auth U] Focus chain W [auth A] Focus chain WA [auth K] Focus chain Y [auth B] Focus chain ZA [auth L] Interactions & Density Focus chain BB [auth M] Focus chain CA [auth C] Focus chain DA [auth D] Focus chain EB [auth N] Focus chain GA [auth E] Focus chain GB [auth O] Focus chain IB [auth P] Focus chain JA [auth F] Focus chain KB [auth Q] Focus chain LB [auth R] Focus chain MA [auth G] Focus chain NA [auth H] Focus chain OB [auth S] Focus chain QA [auth I] Focus chain SA [auth J] Focus chain SB [auth T] Focus chain VB [auth U] Focus chain W [auth A] Focus chain WA [auth K] Focus chain Y [auth B] Focus chain ZA [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.242 (Depositor), 0.246 (DCC)
R-Value Work: 0.204 (Depositor), 0.212 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.226	α = 90
b = 127.924	β = 90
c = 353.843	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-10-19

Deposition Author(s):

Diaz-Saez, L.

Pankov, G.

Hunter, W.N.

Revision History (Full details and data files)

Version 1.0: 2016-10-19
Type: Initial release
Version 1.1: 2017-03-15
Changes: Database references
Version 1.2: 2019-03-06
Changes: Advisory, Data collection, Experimental preparation
Version 1.3: 2019-05-08
Changes: Data collection, Experimental preparation
Version 1.4: 2024-05-01
Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description