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- PDB-4u0h: Crystal Structure of M. tuberculosis ClpP1P1 -

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Basic information

Entry
Database: PDB / ID: 4u0h
TitleCrystal Structure of M. tuberculosis ClpP1P1
ComponentsATP-dependent Clp protease proteolytic subunit 1
KeywordsHYDROLASE / peptidase
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 / plasma membrane / cytosol
Similarity search - Function
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 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2479 Å
AuthorsSchmitz, K.R. / Carney, D.W. / Sello, J.K. / Sauer, R.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-101988 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Crystal structure of Mycobacterium tuberculosis ClpP1P2 suggests a model for peptidase activation by AAA+ partner binding and substrate delivery.
Authors: Schmitz, K.R. / Carney, D.W. / Sello, J.K. / Sauer, R.T.
History
DepositionJul 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references
Revision 1.2Nov 12, 2014Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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 1
B: ATP-dependent Clp protease proteolytic subunit 1
C: ATP-dependent Clp protease proteolytic subunit 1
D: ATP-dependent Clp protease proteolytic subunit 1
E: ATP-dependent Clp protease proteolytic subunit 1
F: ATP-dependent Clp protease proteolytic subunit 1
G: ATP-dependent Clp protease proteolytic subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,43321
Polymers150,0887
Non-polymers1,34514
Water61334
1
A: ATP-dependent Clp protease proteolytic subunit 1
B: ATP-dependent Clp protease proteolytic subunit 1
C: ATP-dependent Clp protease proteolytic subunit 1
D: ATP-dependent Clp protease proteolytic subunit 1
E: ATP-dependent Clp protease proteolytic subunit 1
F: ATP-dependent Clp protease proteolytic subunit 1
G: ATP-dependent Clp protease proteolytic subunit 1
hetero molecules

A: ATP-dependent Clp protease proteolytic subunit 1
B: ATP-dependent Clp protease proteolytic subunit 1
C: ATP-dependent Clp protease proteolytic subunit 1
D: ATP-dependent Clp protease proteolytic subunit 1
E: ATP-dependent Clp protease proteolytic subunit 1
F: ATP-dependent Clp protease proteolytic subunit 1
G: ATP-dependent Clp protease proteolytic subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,86542
Polymers300,17514
Non-polymers2,69028
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area50130 Å2
ΔGint-629 kcal/mol
Surface area85650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.926, 178.926, 265.251
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and resid 14:190
21chain B and resid 14:190
31chain C and resid 14:190
41chain D and resid 14:190
51chain E and resid 14:190
61chain F and resid 14:190
71chain G and resid 14:190

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 14 - 190 / Label seq-ID: 8 - 184

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and resid 14:190AA
2chain B and resid 14:190BB
3chain C and resid 14:190CC
4chain D and resid 14:190DD
5chain E and resid 14:190EE
6chain F and resid 14:190FF
7chain G and resid 14:190GG

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Components

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


Mass: 21441.100 Da / Num. of mol.: 7 / Fragment: mature enzyme
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: clpP1, clpP, Rv2461c, MTV008.17c / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WPC5, endopeptidase Clp
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 4.08 Å3/Da / Density % sol: 69.88 %
Description: 50x50x200 micron rods with hexagonal cross-section
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1:1 mixture of reservoir (1.5 M (NH4)2SO4, 0.1 M MES) and protein solution (2.5 mg/mL ClpP1, 2.5 mg/mL ClpP2, 0.2 mM ADEP-2B5Me, 0.5 mM Z-Ile-Leu, 10 mM HEPES, 50 mM NaCl, 0.5 mM TCEP, 15% DMSO)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.2479→50 Å / Num. obs: 39757 / % possible obs: 98.8 % / Redundancy: 6 % / Biso Wilson estimate: 37.79 Å2 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.082 / Rrim(I) all: 0.209 / Χ2: 0.995 / Net I/av σ(I): 12.817 / Net I/σ(I): 5.3 / Num. measured all: 240307
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2479-3.316.30.51419550.9110.2170.5590.84498.7
3.31-3.376.20.44619300.9380.1880.4850.83498.8
3.37-3.436.20.39419550.9420.1670.4290.83999
3.43-3.56.20.36119450.9590.1530.3930.84498.8
3.5-3.586.20.32319630.9580.1370.3520.87999
3.58-3.666.20.29819480.9590.1260.3240.8999
3.66-3.756.20.25519650.970.1080.2770.9398.8
3.75-3.856.20.25719620.9720.1090.280.88199
3.85-3.976.20.21319680.9770.0910.2320.95399
3.97-4.096.10.1819490.9840.0770.1960.95598.8
4.09-4.246.10.15819770.9850.0670.1721.06199.1
4.24-4.416.10.13919740.9890.0590.1511.10499
4.41-4.616.10.14119790.990.0610.1541.08298.9
4.61-4.856.10.14220060.9890.0610.1551.09999.2
4.85-5.1660.15920000.9870.0690.1731.08899.4
5.16-5.565.90.18519980.9790.080.2021.03199.3
5.56-6.115.80.1820290.9820.0790.1970.99599.4
6.11-75.70.15220390.9860.0670.1671.02799
7-8.815.70.0920790.9950.0390.0981.16899.1
8.81-505.40.05921360.9960.0270.0651.45694.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation8.52 Å30.99 Å
Translation8.52 Å30.99 Å

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1760)refinement
HKL-2000data scaling
HKL-2000data reduction
Cootmodel building
PDB_EXTRACT3.14data extraction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2479→30.991 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2142 1994 5.02 %Random selection
Rwork0.1796 37715 --
obs0.1813 39709 98.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 171.03 Å2 / Biso mean: 26.6287 Å2 / Biso min: 0.5 Å2
Refinement stepCycle: final / Resolution: 3.2479→30.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9426 0 70 34 9530
Biso mean--79.59 12.81 -
Num. residues----1232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039632
X-RAY DIFFRACTIONf_angle_d0.63113021
X-RAY DIFFRACTIONf_chiral_restr0.0261482
X-RAY DIFFRACTIONf_plane_restr0.0021673
X-RAY DIFFRACTIONf_dihedral_angle_d10.7533486
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6529X-RAY DIFFRACTION4.771TORSIONAL
12B6529X-RAY DIFFRACTION4.771TORSIONAL
13C6529X-RAY DIFFRACTION4.771TORSIONAL
14D6529X-RAY DIFFRACTION4.771TORSIONAL
15E6529X-RAY DIFFRACTION4.771TORSIONAL
16F6529X-RAY DIFFRACTION4.771TORSIONAL
17G6529X-RAY DIFFRACTION4.771TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2479-3.32910.32881330.24742643277699
3.3291-3.4190.26991280.23792630275899
3.419-3.51940.2661580.22052648280699
3.5194-3.63290.23411400.20792623276399
3.6329-3.76250.25851430.18122670281399
3.7625-3.91290.23021370.18752648278599
3.9129-4.09060.20091350.16662665280099
4.0906-4.30570.16321650.13722656282199
4.3057-4.57470.18171440.13712679282399
4.5747-4.92660.1771570.14382687284499
4.9266-5.420.19941290.17722742287199
5.42-6.19880.20791530.19082727288099
6.1988-7.78930.21171180.18132811292999
7.7893-30.99230.18851540.1742886304098

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