3P2L | pdb_00003p2l

Crystal Structure of ATP-dependent Clp protease subunit P from Francisella tularensis

PDB DOI: https://doi.org/10.2210/pdb3P2L/pdb

Classification: HYDROLASE
Organism(s): Francisella tularensis subsp. tularensis SCHU S4
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-10-02 Released: 2010-10-20
Deposition Author(s): Kim, Y., Zhou, M., Gu, M., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.226 (Depositor), 0.224 (DCC)
R-Value Work:
0.186 (Depositor), 0.184 (DCC)
R-Value Observed:
0.188 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of ATP-dependent Clp protease subunit P from Francisella tularensis

Kim, Y., Zhou, M., Gu, M., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 162.6 kDa
Atom Count: 10,751
Modeled Residue Count: 1,295
Deposited Residue Count: 1,407
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	201	Francisella tularensis subsp. tularensis SCHU S4	Mutation(s): 0 Gene Names: clpP, FTT_0624 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain WA [auth E] SDF format, chain W [auth B] SDF format, chain VA [auth E] SDF format, chain V [auth B] SDF format, chain UA [auth E] SDF format, chain TA [auth E] SDF format, chain QA [auth D] SDF format, chain PB [auth G] SDF format, chain OA [auth D] SDF format, chain MB [auth G] SDF format, chain MA [auth D] SDF format, chain M [auth A] SDF format, chain LB [auth G] SDF format, chain LA [auth D] SDF format, chain KB [auth G] SDF format, chain K [auth A] SDF format, chain JB [auth G] SDF format, chain I [auth A] SDF format, chain GB [auth F] SDF format, chain GA [auth C] SDF format, chain EA [auth C] SDF format, chain DB [auth F] SDF format, chain DA [auth C] SDF format, chain CB [auth F] SDF format, chain BA [auth B] MOL2 format, chain X [auth B] MOL2 format, chain WA [auth E] MOL2 format, chain W [auth B] MOL2 format, chain VA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth E] MOL2 format, chain TA [auth E] MOL2 format, chain QA [auth D] MOL2 format, chain PB [auth G] MOL2 format, chain OA [auth D] MOL2 format, chain MB [auth G] MOL2 format, chain MA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain LB [auth G] MOL2 format, chain LA [auth D] MOL2 format, chain KB [auth G] MOL2 format, chain K [auth A] MOL2 format, chain JB [auth G] MOL2 format, chain I [auth A] MOL2 format, chain GB [auth F] MOL2 format, chain GA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain DB [auth F] MOL2 format, chain DA [auth C] MOL2 format, chain CB [auth F] MOL2 format, chain BA [auth B] mmCIF format, chain X [auth B] mmCIF format, chain WA [auth E] mmCIF format, chain W [auth B] mmCIF format, chain VA [auth E] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth E] mmCIF format, chain TA [auth E] mmCIF format, chain QA [auth D] mmCIF format, chain PB [auth G] mmCIF format, chain OA [auth D] mmCIF format, chain MB [auth G] mmCIF format, chain MA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain LB [auth G] mmCIF format, chain LA [auth D] mmCIF format, chain KB [auth G] mmCIF format, chain K [auth A] mmCIF format, chain JB [auth G] mmCIF format, chain I [auth A] mmCIF format, chain GB [auth F] mmCIF format, chain GA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain DB [auth F] mmCIF format, chain DA [auth C] mmCIF format, chain CB [auth F] mmCIF format, chain BA [auth B]	BA [auth B] CB [auth F] DA [auth C] DB [auth F] EA [auth C] BA [auth B], CB [auth F], DA [auth C], DB [auth F], EA [auth C], GA [auth C], GB [auth F], I [auth A], JB [auth G], K [auth A], KB [auth G], LA [auth D], LB [auth G], M [auth A], MA [auth D], MB [auth G], OA [auth D], PB [auth G], QA [auth D], TA [auth E], UA [auth E], V [auth B], VA [auth E], W [auth B], WA [auth E], X [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain CB [auth F] Focus chain DA [auth C] Focus chain DB [auth F] Focus chain EA [auth C] Focus chain GA [auth C] Focus chain GB [auth F] Focus chain I [auth A] Focus chain JB [auth G] Focus chain K [auth A] Focus chain KB [auth G] Focus chain LA [auth D] Focus chain LB [auth G] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MB [auth G] Focus chain OA [auth D] Focus chain PB [auth G] Focus chain QA [auth D] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Focus chain WA [auth E] Focus chain X [auth B] Interactions & Density Focus chain BA [auth B] Focus chain CB [auth F] Focus chain DA [auth C] Focus chain DB [auth F] Focus chain EA [auth C] Focus chain GA [auth C] Focus chain GB [auth F] Focus chain I [auth A] Focus chain JB [auth G] Focus chain K [auth A] Focus chain KB [auth G] Focus chain LA [auth D] Focus chain LB [auth G] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MB [auth G] Focus chain OA [auth D] Focus chain PB [auth G] Focus chain QA [auth D] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Focus chain WA [auth E] Focus chain X [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain RB [auth G] SDF format, chain RA [auth D] SDF format, chain R [auth A] SDF format, chain NB [auth G] SDF format, chain JA [auth C] SDF format, chain HB [auth F] SDF format, chain AB [auth E] SDF format, chain AA [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain RB [auth G] MOL2 format, chain RA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain NB [auth G] MOL2 format, chain JA [auth C] MOL2 format, chain HB [auth F] MOL2 format, chain AB [auth E] MOL2 format, chain AA [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain RB [auth G] mmCIF format, chain RA [auth D] mmCIF format, chain R [auth A] mmCIF format, chain NB [auth G] mmCIF format, chain JA [auth C] mmCIF format, chain HB [auth F] mmCIF format, chain AB [auth E] mmCIF format, chain AA [auth B]	AA [auth B] AB [auth E] HB [auth F] JA [auth C] NB [auth G] AA [auth B], AB [auth E], HB [auth F], JA [auth C], NB [auth G], R [auth A], RA [auth D], RB [auth G], T [auth B], U [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth B] Focus chain AB [auth E] Focus chain HB [auth F] Focus chain JA [auth C] Focus chain NB [auth G] Focus chain R [auth A] Focus chain RA [auth D] Focus chain RB [auth G] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth E] Focus chain HB [auth F] Focus chain JA [auth C] Focus chain NB [auth G] Focus chain R [auth A] Focus chain RA [auth D] Focus chain RB [auth G] Focus chain T [auth B] Focus chain U [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain ZA [auth E] SDF format, chain Z [auth B] SDF format, chain YA [auth E] SDF format, chain Y [auth B] SDF format, chain XA [auth E] SDF format, chain QB [auth G] SDF format, chain Q [auth A] SDF format, chain PA [auth D] SDF format, chain O [auth A] SDF format, chain NA [auth D] SDF format, chain L [auth A] SDF format, chain J [auth A] SDF format, chain IA [auth C] SDF format, chain FA [auth C] SDF format, chain EB [auth F] MOL2 format, chain ZA [auth E] MOL2 format, chain Z [auth B] MOL2 format, chain YA [auth E] MOL2 format, chain Y [auth B] MOL2 format, chain XA [auth E] MOL2 format, chain QB [auth G] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain EB [auth F] mmCIF format, chain ZA [auth E] mmCIF format, chain Z [auth B] mmCIF format, chain YA [auth E] mmCIF format, chain Y [auth B] mmCIF format, chain XA [auth E] mmCIF format, chain QB [auth G] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain EB [auth F]	EB [auth F] FA [auth C] IA [auth C] J [auth A] L [auth A] EB [auth F], FA [auth C], IA [auth C], J [auth A], L [auth A], NA [auth D], O [auth A], PA [auth D], Q [auth A], QB [auth G], XA [auth E], Y [auth B], YA [auth E], Z [auth B], ZA [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EB [auth F] Focus chain FA [auth C] Focus chain IA [auth C] Focus chain J [auth A] Focus chain L [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QB [auth G] Focus chain XA [auth E] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain Z [auth B] Focus chain ZA [auth E] Interactions & Density Focus chain EB [auth F] Focus chain FA [auth C] Focus chain IA [auth C] Focus chain J [auth A] Focus chain L [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QB [auth G] Focus chain XA [auth E] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain Z [auth B] Focus chain ZA [auth E]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain OB [auth G] SDF format, chain N [auth A] SDF format, chain HA [auth C] SDF format, chain FB [auth F] MOL2 format, chain P [auth A] MOL2 format, chain OB [auth G] MOL2 format, chain N [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain FB [auth F] mmCIF format, chain P [auth A] mmCIF format, chain OB [auth G] mmCIF format, chain N [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain FB [auth F]	FB [auth F], HA [auth C], N [auth A], OB [auth G], P [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain FB [auth F] Focus chain HA [auth C] Focus chain N [auth A] Focus chain OB [auth G] Focus chain P [auth A] Interactions & Density Focus chain FB [auth F] Focus chain HA [auth C] Focus chain N [auth A] Focus chain OB [auth G] Focus chain P [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain SA [auth E] SDF format, chain S [auth B] SDF format, chain KA [auth D] SDF format, chain IB [auth G] SDF format, chain H [auth A] SDF format, chain CA [auth C] SDF format, chain BB [auth F] MOL2 format, chain SA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain KA [auth D] MOL2 format, chain IB [auth G] MOL2 format, chain H [auth A] MOL2 format, chain CA [auth C] MOL2 format, chain BB [auth F] mmCIF format, chain SA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain KA [auth D] mmCIF format, chain IB [auth G] mmCIF format, chain H [auth A] mmCIF format, chain CA [auth C] mmCIF format, chain BB [auth F]	BB [auth F] CA [auth C] H [auth A] IB [auth G] KA [auth D] BB [auth F], CA [auth C], H [auth A], IB [auth G], KA [auth D], S [auth B], SA [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BB [auth F] Focus chain CA [auth C] Focus chain H [auth A] Focus chain IB [auth G] Focus chain KA [auth D] Focus chain S [auth B] Focus chain SA [auth E] Interactions & Density Focus chain BB [auth F] Focus chain CA [auth C] Focus chain H [auth A] Focus chain IB [auth G] Focus chain KA [auth D] Focus chain S [auth B] Focus chain SA [auth E]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.226 (Depositor), 0.224 (DCC)
R-Value Work: 0.186 (Depositor), 0.184 (DCC)
R-Value Observed: 0.188 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.523	α = 90
b = 128.823	β = 90
c = 98.03	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
RESOLVE	model building
SOLVE	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
RESOLVE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-10-20

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-10-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary