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- PDB-6w9t: Crystal structure of Neisseria meningitidis ClpP protease complex... -

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Basic information

Entry
Database: PDB / ID: 6w9t
TitleCrystal structure of Neisseria meningitidis ClpP protease complex with small molecule activator ACP1-06
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / Serine protease / proteostasis / activator / complex / antibacterial drugs
Function / homology
Function and homology information


endopeptidase Clp complex / endopeptidase Clp / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / proteolysis / cytoplasm
Similarity search - Function
ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
: / Chem-KHS / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsMabanglo, M.F. / Houry, W.A.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-148564 Canada
CitationJournal: Acs Infect Dis. / Year: 2020
Title: Development of Antibiotics That Dysregulate the Neisserial ClpP Protease.
Authors: Binepal, G. / Mabanglo, M.F. / Goodreid, J.D. / Leung, E. / Barghash, M.M. / Wong, K.S. / Lin, F. / Cossette, M. / Bansagi, J. / Song, B. / Balasco Serrao, V.H. / Pai, E.F. / Batey, R.A. / ...Authors: Binepal, G. / Mabanglo, M.F. / Goodreid, J.D. / Leung, E. / Barghash, M.M. / Wong, K.S. / Lin, F. / Cossette, M. / Bansagi, J. / Song, B. / Balasco Serrao, V.H. / Pai, E.F. / Batey, R.A. / Gray-Owen, S.D. / Houry, W.A.
History
DepositionMar 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent Clp protease proteolytic subunit
B: ATP-dependent Clp protease proteolytic subunit
C: ATP-dependent Clp protease proteolytic subunit
D: ATP-dependent Clp protease proteolytic subunit
E: ATP-dependent Clp protease proteolytic subunit
F: ATP-dependent Clp protease proteolytic subunit
G: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,68815
Polymers154,9477
Non-polymers7418
Water12,683704
1
A: ATP-dependent Clp protease proteolytic subunit
B: ATP-dependent Clp protease proteolytic subunit
C: ATP-dependent Clp protease proteolytic subunit
D: ATP-dependent Clp protease proteolytic subunit
E: ATP-dependent Clp protease proteolytic subunit
F: ATP-dependent Clp protease proteolytic subunit
G: ATP-dependent Clp protease proteolytic subunit
hetero molecules

A: ATP-dependent Clp protease proteolytic subunit
B: ATP-dependent Clp protease proteolytic subunit
C: ATP-dependent Clp protease proteolytic subunit
D: ATP-dependent Clp protease proteolytic subunit
E: ATP-dependent Clp protease proteolytic subunit
F: ATP-dependent Clp protease proteolytic subunit
G: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,37630
Polymers309,89514
Non-polymers1,48116
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545x,-y-1,-z1
Unit cell
Length a, b, c (Å)97.328, 119.150, 127.763
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11E-485-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 23 through 131 or resid 137 through 200))
21(chain B and (resid 23 through 131 or resid 137 through 200))
31(chain C and (resid 23 through 131 or resid 137 through 200))
41(chain D and (resid 23 through 131 or resid 137 through 200))
51(chain E and (resid 23 through 131 or resid 137 through 200))
61(chain F and resid 23 through 200)
71(chain G and resid 23 through 200)

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPILEILE(chain A and (resid 23 through 131 or resid 137 through 200))AA23 - 13118 - 126
12GLYGLYALAALA(chain A and (resid 23 through 131 or resid 137 through 200))AA137 - 200132 - 195
21ASPASPILEILE(chain B and (resid 23 through 131 or resid 137 through 200))BB23 - 13118 - 126
22GLYGLYALAALA(chain B and (resid 23 through 131 or resid 137 through 200))BB137 - 200132 - 195
31ASPASPILEILE(chain C and (resid 23 through 131 or resid 137 through 200))CC23 - 13118 - 126
32GLYGLYALAALA(chain C and (resid 23 through 131 or resid 137 through 200))CC137 - 200132 - 195
41ASPASPILEILE(chain D and (resid 23 through 131 or resid 137 through 200))DD23 - 13118 - 126
42GLYGLYALAALA(chain D and (resid 23 through 131 or resid 137 through 200))DD137 - 200132 - 195
51ASPASPILEILE(chain E and (resid 23 through 131 or resid 137 through 200))EE23 - 13118 - 126
52GLYGLYALAALA(chain E and (resid 23 through 131 or resid 137 through 200))EE137 - 200132 - 195
61ASPASPALAALA(chain F and resid 23 through 200)FF23 - 20018 - 195
71ASPASPALAALA(chain G and resid 23 through 200)GG23 - 20018 - 195

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Components

#1: Protein
ATP-dependent Clp protease proteolytic subunit / / Endopeptidase Clp


Mass: 22135.324 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: clpP, COI09_01760, ERS514410_00057 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0Y5K536, UniProt: Q9JZ38*PLUS, endopeptidase Clp
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-KHS / N-{2-[(2-chlorophenyl)sulfanyl]ethyl}-2-methyl-2-{[5-(trifluoromethyl)pyridin-2-yl]sulfonyl}propanamide


Mass: 466.925 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18ClF3N2O3S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 704 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M sodium acetate, 40% 2-methyl-2,4-pentanediol (MPD)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1 Å
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Jul 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→119.15 Å / Num. obs: 179842 / % possible obs: 98.2 % / Redundancy: 5.6 % / CC1/2: 0.984 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.067 / Rrim(I) all: 0.16 / Net I/σ(I): 12.1 / Num. measured all: 1012426 / Scaling rejects: 15354
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.64-1.662.10.5651437866910.4650.4260.712175.1
8.96-119.1560.066760812770.9960.0280.0723299.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NB1

6nb1


Resolution: 1.64→97.33 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 32.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2816 2010 1.12 %
Rwork0.2373 177760 -
obs0.2378 179770 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 200.83 Å2 / Biso mean: 35.0506 Å2 / Biso min: 6.47 Å2
Refinement stepCycle: final / Resolution: 1.64→97.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9775 0 101 704 10580
Biso mean--65.68 36.68 -
Num. residues----1249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0129971
X-RAY DIFFRACTIONf_angle_d1.28213428
X-RAY DIFFRACTIONf_dihedral_angle_d17.4211343
X-RAY DIFFRACTIONf_chiral_restr0.0621527
X-RAY DIFFRACTIONf_plane_restr0.0081742
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3661X-RAY DIFFRACTION7.591TORSIONAL
12B3661X-RAY DIFFRACTION7.591TORSIONAL
13C3661X-RAY DIFFRACTION7.591TORSIONAL
14D3661X-RAY DIFFRACTION7.591TORSIONAL
15E3661X-RAY DIFFRACTION7.591TORSIONAL
16F3661X-RAY DIFFRACTION7.591TORSIONAL
17G3661X-RAY DIFFRACTION7.591TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.64-1.680.4081150.3842103671048281
1.68-1.720.38471430.3537122941243796
1.72-1.770.35781370.31791281212949100
1.77-1.830.3351460.30061280712953100
1.83-1.890.33061490.28321281212961100
1.89-1.970.32241420.27741282912971100
1.97-2.060.32081540.27271288813042100
2.06-2.170.30361390.26981284312982100
2.17-2.30.31991480.25581283912987100
2.3-2.480.30041430.24911295313096100
2.48-2.730.25241460.24111291313059100
2.73-3.130.30231450.2267129361308199
3.13-3.940.23771460.2021304813194100
3.94-97.330.23791570.1927134191357699
Refinement TLS params.Method: refined / Origin x: -22.681 Å / Origin y: -44.0536 Å / Origin z: 17.2806 Å
111213212223313233
T0.1536 Å2-0.0274 Å2-0.0161 Å2-0.1346 Å2-0.021 Å2--0.0448 Å2
L0.0354 °2-0.114 °2-0.0239 °2-0.6241 °20.0717 °2--0.0525 °2
S0.0089 Å °-0.0057 Å °0.0214 Å °0.3469 Å °-0.0191 Å °0.1299 Å °-0.0769 Å °-0.0314 Å °0.0368 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA7 - 201
2X-RAY DIFFRACTION1allB7 - 200
3X-RAY DIFFRACTION1allC8 - 202
4X-RAY DIFFRACTION1allD8 - 203
5X-RAY DIFFRACTION1allE23 - 200
6X-RAY DIFFRACTION1allF8 - 201
7X-RAY DIFFRACTION1allG23 - 201
8X-RAY DIFFRACTION1allX1
9X-RAY DIFFRACTION1allY1 - 7
10X-RAY DIFFRACTION1allZ1 - 889

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