6MX2 | pdb_00006mx2

Crystal Structure of ClpP1 from Clostridium difficile 630.

PDB DOI: https://doi.org/10.2210/pdb6MX2/pdb

Classification: HYDROLASE
Organism(s): Clostridioides difficile 630
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-10-30 Released: 2018-11-14
Deposition Author(s): Lavey, N.P., Thomas, L.M., Duerfeldt, A.S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.244 (Depositor), 0.245 (DCC)
R-Value Work:
0.193 (Depositor), 0.194 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of ClpP1 from Clostridium difficile 630.

Lavey, N.P., Thomas, L.M., Duerfeldt, A.S.

To be published.

Macromolecule Content

Total Structure Weight: 299.04 kDa
Atom Count: 20,432
Modeled Residue Count: 2,551
Deposited Residue Count: 2,716
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	194	Clostridioides difficile 630	Mutation(s): 0 Gene Names: clpP1, clpP, CD630_33050 EC: 3.4.21.92
UniProt
Find proteins for Q180F0 (Clostridioides difficile (strain 630)) Explore Q180F0 Go to UniProtKB: Q180F0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q180F0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain FA [auth N] SDF format, chain DA [auth M] MOL2 format, chain FA [auth N] MOL2 format, chain DA [auth M] mmCIF format, chain FA [auth N] mmCIF format, chain DA [auth M]	DA [auth M], FA [auth N]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DA [auth M] Focus chain FA [auth N] Interactions & Density Focus chain DA [auth M] Focus chain FA [auth N]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain Z [auth J] SDF format, chain Y [auth I] SDF format, chain X [auth I] SDF format, chain W [auth H] SDF format, chain V [auth G] SDF format, chain U [auth G] SDF format, chain T [auth F] SDF format, chain S [auth E] 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 GA [auth N] SDF format, chain EA [auth M] SDF format, chain CA [auth L] SDF format, chain BA [auth L] SDF format, chain AA [auth K] MOL2 format, chain Z [auth J] MOL2 format, chain Y [auth I] MOL2 format, chain X [auth I] MOL2 format, chain W [auth H] MOL2 format, chain V [auth G] MOL2 format, chain U [auth G] MOL2 format, chain T [auth F] MOL2 format, chain S [auth E] 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 GA [auth N] MOL2 format, chain EA [auth M] MOL2 format, chain CA [auth L] MOL2 format, chain BA [auth L] MOL2 format, chain AA [auth K] mmCIF format, chain Z [auth J] mmCIF format, chain Y [auth I] mmCIF format, chain X [auth I] mmCIF format, chain W [auth H] mmCIF format, chain V [auth G] mmCIF format, chain U [auth G] mmCIF format, chain T [auth F] mmCIF format, chain S [auth E] 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 GA [auth N] mmCIF format, chain EA [auth M] mmCIF format, chain CA [auth L] mmCIF format, chain BA [auth L] mmCIF format, chain AA [auth K]	AA [auth K] BA [auth L] CA [auth L] EA [auth M] GA [auth N] AA [auth K], BA [auth L], CA [auth L], EA [auth M], GA [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 G], W [auth H], X [auth I], Y [auth I], Z [auth J]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth K] Focus chain BA [auth L] Focus chain CA [auth L] Focus chain EA [auth M] Focus chain GA [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 G] Focus chain W [auth H] Focus chain X [auth I] Focus chain Y [auth I] Focus chain Z [auth J] Interactions & Density Focus chain AA [auth K] Focus chain BA [auth L] Focus chain CA [auth L] Focus chain EA [auth M] Focus chain GA [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 G] Focus chain W [auth H] Focus chain X [auth I] Focus chain Y [auth I] Focus chain Z [auth J]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.244 (Depositor), 0.245 (DCC)
R-Value Work: 0.193 (Depositor), 0.194 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.328	α = 113.15
b = 97.372	β = 104.56
c = 106.494	γ = 103.21

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-11-14

Deposition Author(s):

Lavey, N.P.

Thomas, L.M.

Duerfeldt, A.S.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20GM103640

Revision History (Full details and data files)

Version 1.0: 2018-11-14
Type: Initial release
Version 1.1: 2019-01-23
Changes: Data collection, Database references, Source and taxonomy, Structure summary
Version 1.2: 2020-01-01
Changes: Author supporting evidence
Version 1.3: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description