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- PDB-4jct: ClpP2 from Listeria monocytogenes -

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Basic information

Entry
Database: PDB / ID: 4jct
TitleClpP2 from Listeria monocytogenes
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / Pathogenic bacteria / Virulence factor / regulation / CLP protease family / inactive catalytic triad
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
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZeiler, E. / List, A. / Alte, F. / Gersch, M. / Wachtel, R. / Groll, M. / Sieber, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural and functional insights into caseinolytic proteases reveal an unprecedented regulation principle of their catalytic triad.
Authors: Zeiler, E. / List, A. / Alte, F. / Gersch, M. / Wachtel, R. / Poreba, M. / Drag, M. / Groll, M. / Sieber, S.A.
History
DepositionFeb 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Sep 20, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)160,7997
Polymers160,7997
Non-polymers00
Water5,062281
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

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


Theoretical massNumber of molelcules
Total (without water)321,59814
Polymers321,59814
Non-polymers00
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area56120 Å2
ΔGint-325 kcal/mol
Surface area85640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.110, 148.460, 103.470
Angle α, β, γ (deg.)90.00, 119.31, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-318-

HOH

21B-333-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.640958, 0.764699, -0.066395), (-0.763981, 0.627204, -0.151486), (-0.074198, 0.14782, 0.986227)19.31693, -9.3466, 3.70737
3given(-0.189854, 0.957348, -0.217811), (-0.954269, -0.232108, -0.188406), (-0.230926, 0.17208, 0.957633)23.91432, -30.46616, 4.56557
4given(-0.836225, 0.42629, -0.34497), (-0.425385, -0.901241, -0.082535), (-0.346085, 0.077727, 0.934978)10.74251, -47.7385, 2.19601
5given(-0.833051, -0.434533, -0.342356), (0.435732, -0.896702, 0.077869), (-0.340827, -0.084307, 0.936338)-10.94235, -47.32066, -1.92206
6given(-0.181322, -0.958183, -0.221376), (0.95774, -0.223165, 0.181471), (-0.223286, -0.179116, 0.958155)-23.98027, -30.78287, -4.41009
7given(0.629857, -0.773639, -0.06902), (0.774215, 0.61823, 0.135582), (-0.062222, -0.138834, 0.988359)-19.24906, -9.57503, -3.48725

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Components

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


Mass: 22971.289 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: ATCC BAA-679 / EGD-e / Gene: clpP, lmo2468 / Plasmid: pDEST GATEWAY / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q9RQI6, endopeptidase Clp
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M Mes, 1.0 M LiCl, 10% PEG6000 , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2011
RadiationMonochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 48709 / Num. obs: 46079 / % possible obs: 94.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.3
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 2 / % possible all: 92.2

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V5E

3v5e


Resolution: 2.6→14.98 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.92 / SU B: 25.886 / SU ML: 0.256 / Cross valid method: THROUGHOUT / ESU R: 1.037 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24833 2292 5 %RANDOM
Rwork0.21068 ---
all0.215 43558 --
obs0.21259 43558 94.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.447 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å2-0.18 Å2
2--0.03 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.6→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9849 0 0 281 10130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.029975
X-RAY DIFFRACTIONr_angle_refined_deg0.9961.97313454
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.95751274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.05425.484434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.786151813
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7821549
X-RAY DIFFRACTIONr_chiral_restr0.0710.21561
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217371
LS refinement shellResolution: 2.6→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.444 154 -
Rwork0.358 2943 -
obs--90.08 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.35150.191-0.35940.4046-0.39950.5063-0.0054-0.00410.01670.00940.02150.0068-0.0037-0.0118-0.01610.0350.0064-0.01750.0422-0.01250.011625.1144-15.171526.4522
20.1185-0.01610.030.2625-0.29230.32820.0046-0.01910.00170.0135-0.0090.0015-0.01590.00590.00450.0292-0.0024-0.00330.0279-0.00670.01826.49694.14722.9357
30.21240.02570.18160.1855-0.14350.3074-0.0242-0.0192-0.0115-0.02470.0216-0.02140.0095-0.03650.00260.03650.01270.00820.0259-0.00860.0236-19.89671.378217.8112
40.12030.00980.21680.4550.14170.4246-0.0024-0.0026-0.00740.00550.00870.03420.0053-0.0009-0.00630.0164-0.01090.01820.0333-0.00850.0229-34.2856-21.327115.0331
50.15390.03110.1370.26160.18970.2259-0.00320.00180.0061-0.0030.0149-0.0194-0.00860.013-0.01170.0317-0.02340.00510.03580.00660.0162-25.7113-46.896216.7323
60.4318-0.1706-0.17750.24020.30090.3817-0.0057-0.0269-0.03870.0110.00610.00240.01270.0103-0.00030.0288-0.0034-0.00490.02450.01630.0129-0.8511-56.064321.535
70.4619-0.0775-0.26530.01320.04280.2094-0.0059-0.01280.01570.0020.0045-0.0035-0.001-0.01290.00140.03980.0179-0.00730.02780.00060.009821.7633-41.952925.7765
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 193
2X-RAY DIFFRACTION2B3 - 193
3X-RAY DIFFRACTION3C3 - 193
4X-RAY DIFFRACTION4D3 - 193
5X-RAY DIFFRACTION5E3 - 193
6X-RAY DIFFRACTION6F3 - 193
7X-RAY DIFFRACTION7G3 - 193

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