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- PDB-6nay: Crystal structure of Neisseria meningitidis ClpP protease E31A+E5... -

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Basic information

Entry
Database: PDB / ID: 6nay
TitleCrystal structure of Neisseria meningitidis ClpP protease E31A+E58A activated double mutant
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / Serine protease / antibiotic
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 / 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 / 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
ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.199 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 6, 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 1.3Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)680,25128
Polymers680,25128
Non-polymers00
Water24,9691386
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
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


Theoretical massNumber of molelcules
Total (without water)340,12614
Polymers340,12614
Non-polymers00
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45830 Å2
ΔGint-181 kcal/mol
Surface area93380 Å2
MethodPISA
2
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


Theoretical massNumber of molelcules
Total (without water)340,12614
Polymers340,12614
Non-polymers00
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area46280 Å2
ΔGint-177 kcal/mol
Surface area92890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.707, 119.840, 127.861
Angle α, β, γ (deg.)90.020, 89.990, 90.020
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 24294.680 Da / Num. of mol.: 28 / Mutation: E31A, E58A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: clpP / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0H5Q9L9, UniProt: Q9JZ38*PLUS, endopeptidase Clp
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1386 / 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: 2.22 Å3/Da / Density % sol: 44.68 %
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 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jun 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.199→50 Å / Num. obs: 283478 / % possible obs: 95.4 % / Redundancy: 1.9 % / Biso Wilson estimate: 31.8 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.5
Reflection shellResolution: 2.199→2.24 Å / Rmerge(I) obs: 0.356 / Num. unique all: 13879 / Num. unique obs: 13879 / CC1/2: 0.769

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DKP

5dkp


Resolution: 2.199→46.046 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 23.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2448 1991 0.7 %
Rwork0.2136 281417 -
obs0.2138 283408 95.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.72 Å2 / Biso mean: 39.7052 Å2 / Biso min: 16.15 Å2
Refinement stepCycle: final / Resolution: 2.199→46.046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38118 0 0 1386 39504
Biso mean---39.15 -
Num. residues----4905
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1993-2.25430.3171410.28281894590
2.2543-2.31520.29641480.26781967693
2.3152-2.38330.29621320.25391974994
2.3833-2.46030.24071380.24081989494
2.4603-2.54820.21371380.23961992194
2.5482-2.65020.291440.23212012195
2.6502-2.77080.24991590.22292008095
2.7708-2.91690.25441570.21532027596
2.9169-3.09960.221180.21822032296
3.0996-3.33880.24911450.21382038097
3.3388-3.67470.24271500.20562051297
3.6747-4.20610.23151320.19412052297
4.2061-5.2980.23741480.18472052897
5.298-46.0460.22551410.21012049297

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