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- PDB-6naq: Crystal structure of Neisseria meningitidis ClpP protease in Apo form -

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Basic information

Entry
Database: PDB / ID: 6naq
TitleCrystal structure of Neisseria meningitidis ClpP protease in Apo form
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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.022 Å
AuthorsHoury, W.A. / Mabanglo, M.F. / Pai, E.F. / Eger, B.T. / Bryson, S.
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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)344,31628
Polymers343,76814
Non-polymers54714
Water11,403633
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area57720 Å2
ΔGint-205 kcal/mol
Surface area92980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.584, 127.945, 120.195
Angle α, β, γ (deg.)90.00, 90.19, 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: 24554.881 Da / Num. of mol.: 14
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: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 633 / 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: 2.38 Å3/Da / Density % sol: 48.36 %
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: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.23894 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jan 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23894 Å / Relative weight: 1
ReflectionResolution: 2.02→51.39 Å / Num. obs: 190314 / % possible obs: 98.2 % / Redundancy: 3.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.097 / Net I/σ(I): 12.2
Reflection shellResolution: 2.02→2.15 Å / Rmerge(I) obs: 0.29 / Num. unique obs: 5570 / CC1/2: 0.949

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DKP

5dkp


Resolution: 2.022→51.39 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.7
RfactorNum. reflection% reflection
Rfree0.2459 9496 5 %
Rwork0.2068 --
obs0.2088 189962 97.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.022→51.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20039 0 14 633 20686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00820327
X-RAY DIFFRACTIONf_angle_d1.15827369
X-RAY DIFFRACTIONf_dihedral_angle_d13.2097697
X-RAY DIFFRACTIONf_chiral_restr0.0483115
X-RAY DIFFRACTIONf_plane_restr0.0063577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0216-2.04460.31192750.26325295X-RAY DIFFRACTION86
2.0446-2.06870.30853070.25485876X-RAY DIFFRACTION96
2.0687-2.09390.28873050.24725978X-RAY DIFFRACTION97
2.0939-2.12040.31323070.24775865X-RAY DIFFRACTION97
2.1204-2.14830.31713110.25195955X-RAY DIFFRACTION96
2.1483-2.17770.28993340.23885930X-RAY DIFFRACTION97
2.1777-2.20880.29573230.23385972X-RAY DIFFRACTION97
2.2088-2.24180.2973620.2355931X-RAY DIFFRACTION97
2.2418-2.27680.28353300.22685925X-RAY DIFFRACTION97
2.2768-2.31420.28733060.23146013X-RAY DIFFRACTION97
2.3142-2.35410.28263080.2326006X-RAY DIFFRACTION98
2.3541-2.39690.27723180.22846009X-RAY DIFFRACTION98
2.3969-2.4430.26573120.21975952X-RAY DIFFRACTION98
2.443-2.49280.28313240.21776056X-RAY DIFFRACTION98
2.4928-2.5470.26853190.21936037X-RAY DIFFRACTION98
2.547-2.60630.24943100.22156047X-RAY DIFFRACTION98
2.6063-2.67150.28163200.21256024X-RAY DIFFRACTION98
2.6715-2.74370.26413480.21236020X-RAY DIFFRACTION98
2.7437-2.82440.26543040.21476067X-RAY DIFFRACTION99
2.8244-2.91560.23793270.20926063X-RAY DIFFRACTION99
2.9156-3.01980.26142880.21336063X-RAY DIFFRACTION99
3.0198-3.14070.24612900.21176145X-RAY DIFFRACTION99
3.1407-3.28360.22612890.21216132X-RAY DIFFRACTION99
3.2836-3.45670.24683150.21526118X-RAY DIFFRACTION99
3.4567-3.67320.25363290.20736117X-RAY DIFFRACTION99
3.6732-3.95670.21423160.18536121X-RAY DIFFRACTION99
3.9567-4.35470.19183330.16666142X-RAY DIFFRACTION99
4.3547-4.98440.17863310.15286162X-RAY DIFFRACTION99
4.9844-6.2780.22763340.20826195X-RAY DIFFRACTION100
6.278-51.40650.19053210.16786250X-RAY DIFFRACTION99

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