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- PDB-6nah: Crystal structure of Neisseria meningitidis ClpP protease in comp... -

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Basic information

Entry
Database: PDB / ID: 6nah
TitleCrystal structure of Neisseria meningitidis ClpP protease in complex with Acyldepsipeptide-14 (ADEP-14)
Components
  • ATP-dependent Clp protease proteolytic subunit
  • Acyldepsipeptide-14
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Serine protease / antibiotic / anticancer / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / 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 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...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 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
OCTANOIC ACID (CAPRYLIC ACID) / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMabanglo, M.F. / Houry, W.A.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)XNE-86945 Canada
Canadian Institutes of Health Research (CIHR)PJT-148564 Canada
CitationJournal: Commun Biol / Year: 2019
Title: ClpP protease activation results from the reorganization of the electrostatic interaction networks at the entrance pores.
Authors: 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. / ...Authors: 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.
History
DepositionDec 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Feb 22, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_mon_prot_cis / struct_ref_seq
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end
Revision 2.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
H: ATP-dependent Clp protease proteolytic subunit
I: ATP-dependent Clp protease proteolytic subunit
J: ATP-dependent Clp protease proteolytic subunit
K: ATP-dependent Clp protease proteolytic subunit
L: ATP-dependent Clp protease proteolytic subunit
M: ATP-dependent Clp protease proteolytic subunit
N: ATP-dependent Clp protease proteolytic subunit
O: ATP-dependent Clp protease proteolytic subunit
P: ATP-dependent Clp protease proteolytic subunit
Q: ATP-dependent Clp protease proteolytic subunit
R: ATP-dependent Clp protease proteolytic subunit
S: ATP-dependent Clp protease proteolytic subunit
T: ATP-dependent Clp protease proteolytic subunit
U: ATP-dependent Clp protease proteolytic subunit
V: ATP-dependent Clp protease proteolytic subunit
W: ATP-dependent Clp protease proteolytic subunit
X: ATP-dependent Clp protease proteolytic subunit
Y: ATP-dependent Clp protease proteolytic subunit
Z: ATP-dependent Clp protease proteolytic subunit
a: ATP-dependent Clp protease proteolytic subunit
b: ATP-dependent Clp protease proteolytic subunit
c: Acyldepsipeptide-14
e: Acyldepsipeptide-14
f: Acyldepsipeptide-14
g: Acyldepsipeptide-14
h: Acyldepsipeptide-14
i: Acyldepsipeptide-14
j: Acyldepsipeptide-14
k: Acyldepsipeptide-14
l: Acyldepsipeptide-14
m: Acyldepsipeptide-14
n: Acyldepsipeptide-14
o: Acyldepsipeptide-14
p: Acyldepsipeptide-14
q: Acyldepsipeptide-14
r: Acyldepsipeptide-14
s: Acyldepsipeptide-14
t: Acyldepsipeptide-14
u: Acyldepsipeptide-14
v: Acyldepsipeptide-14
w: Acyldepsipeptide-14
x: Acyldepsipeptide-14
y: Acyldepsipeptide-14
z: Acyldepsipeptide-14
0: Acyldepsipeptide-14
1: Acyldepsipeptide-14
2: Acyldepsipeptide-14
3: Acyldepsipeptide-14
4: Acyldepsipeptide-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)706,93684
Polymers702,89856
Non-polymers4,03828
Water12,719706
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
c: Acyldepsipeptide-14
e: Acyldepsipeptide-14
f: Acyldepsipeptide-14
g: Acyldepsipeptide-14
h: Acyldepsipeptide-14
i: Acyldepsipeptide-14
j: Acyldepsipeptide-14
hetero molecules

V: ATP-dependent Clp protease proteolytic subunit
W: ATP-dependent Clp protease proteolytic subunit
X: ATP-dependent Clp protease proteolytic subunit
Y: ATP-dependent Clp protease proteolytic subunit
Z: ATP-dependent Clp protease proteolytic subunit
a: ATP-dependent Clp protease proteolytic subunit
b: ATP-dependent Clp protease proteolytic subunit
y: Acyldepsipeptide-14
z: Acyldepsipeptide-14
0: Acyldepsipeptide-14
1: Acyldepsipeptide-14
2: Acyldepsipeptide-14
3: Acyldepsipeptide-14
4: Acyldepsipeptide-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)353,46842
Polymers351,44928
Non-polymers2,01914
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
2
H: ATP-dependent Clp protease proteolytic subunit
I: ATP-dependent Clp protease proteolytic subunit
J: ATP-dependent Clp protease proteolytic subunit
K: ATP-dependent Clp protease proteolytic subunit
L: ATP-dependent Clp protease proteolytic subunit
M: ATP-dependent Clp protease proteolytic subunit
N: ATP-dependent Clp protease proteolytic subunit
O: ATP-dependent Clp protease proteolytic subunit
P: ATP-dependent Clp protease proteolytic subunit
Q: ATP-dependent Clp protease proteolytic subunit
R: ATP-dependent Clp protease proteolytic subunit
S: ATP-dependent Clp protease proteolytic subunit
T: ATP-dependent Clp protease proteolytic subunit
U: ATP-dependent Clp protease proteolytic subunit
k: Acyldepsipeptide-14
l: Acyldepsipeptide-14
m: Acyldepsipeptide-14
n: Acyldepsipeptide-14
o: Acyldepsipeptide-14
p: Acyldepsipeptide-14
q: Acyldepsipeptide-14
r: Acyldepsipeptide-14
s: Acyldepsipeptide-14
t: Acyldepsipeptide-14
u: Acyldepsipeptide-14
v: Acyldepsipeptide-14
w: Acyldepsipeptide-14
x: Acyldepsipeptide-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)353,46842
Polymers351,44928
Non-polymers2,01914
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.238, 195.976, 139.894
Angle α, β, γ (deg.)90.00, 97.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 24410.754 Da / Num. of mol.: 28
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: clpP / Production host: Escherichia coli (E. coli)
References: UniProt: I4E574, UniProt: Q9JZ38*PLUS, endopeptidase Clp
#2: Protein/peptide ...
Acyldepsipeptide-14


Mass: 692.750 Da / Num. of mol.: 28 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical...
ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID)


Mass: 144.211 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C8H16O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 706 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M potassium thiocyanate 40% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Mar 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 168533 / % possible obs: 98.7 % / Redundancy: 3.8 % / Net I/σ(I): 7.6
Reflection shellResolution: 2.7→2.75 Å / Rmerge(I) obs: 0.92 / Num. unique obs: 8280 / CC1/2: 0.559 / Rpim(I) all: 0.543 / Rrim(I) all: 1.07

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DKP

5dkp


Resolution: 2.7→49.631 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2479 1999 1.19 %
Rwork0.1922 --
obs0.1928 168440 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→49.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37775 0 1596 706 40077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0140017
X-RAY DIFFRACTIONf_angle_d1.44453945
X-RAY DIFFRACTIONf_dihedral_angle_d11.70424015
X-RAY DIFFRACTIONf_chiral_restr0.0696084
X-RAY DIFFRACTIONf_plane_restr0.0087003
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7022-2.76970.30211380.231511475X-RAY DIFFRACTION96
2.7697-2.84460.31661420.220211799X-RAY DIFFRACTION98
2.8446-2.92830.26181410.204411802X-RAY DIFFRACTION98
2.9283-3.02280.27791420.207511787X-RAY DIFFRACTION98
3.0228-3.13080.27211420.200311836X-RAY DIFFRACTION98
3.1308-3.25620.28111420.19111872X-RAY DIFFRACTION98
3.2562-3.40430.24461430.184811875X-RAY DIFFRACTION99
3.4043-3.58380.24611430.189711899X-RAY DIFFRACTION99
3.5838-3.80820.26851440.183411935X-RAY DIFFRACTION99
3.8082-4.10210.19821420.168811931X-RAY DIFFRACTION99
4.1021-4.51470.22821460.170112044X-RAY DIFFRACTION99
4.5147-5.16740.2251440.183712021X-RAY DIFFRACTION100
5.1674-6.50810.27811450.237512088X-RAY DIFFRACTION100
6.5081-49.63930.22831450.191512077X-RAY DIFFRACTION99

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