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- PDB-4jcr: ClpP1 N165D mutant from Listeria monocytogenes -

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Basic information

Entry
Database: PDB / ID: 4jcr
TitleClpP1 N165D mutant from Listeria monocytogenes
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / Pathogenic bacteria / Virulence factor / regulation / CLP protease family / active 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, 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: 2.1 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
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)317,83614
Polymers317,83614
Non-polymers00
Water21,2761181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41990 Å2
ΔGint-195 kcal/mol
Surface area93180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.270, 147.410, 109.320
Angle α, β, γ (deg.)90.00, 90.26, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.617441, 0.689364, -0.378872), (-0.665435, 0.714592, 0.215764), (0.419479, 0.118894, 0.899945)27.77944, 6.4496, -5.87357
3given(-0.215639, 0.880426, -0.422314), (-0.79934, 0.089248, 0.594214), (0.560853, 0.465708, 0.684514)50.40057, -8.2072, 0.9191
4given(-0.89816, 0.426261, -0.107748), (-0.303454, -0.42366, 0.85348), (0.318156, 0.799258, 0.509866)53.02569, -32.64094, 15.04654
5given(-0.891508, -0.315516, 0.325058), (0.437306, -0.412149, 0.799311), (-0.118223, 0.854742, 0.505411)32.35341, -49.09665, 26.24162
6given(-0.225339, -0.792145, 0.567211), (0.881478, 0.082219, 0.465013), (-0.414994, 0.604769, 0.679731)3.65158, -44.4061, 25.92725
7given(0.627164, -0.660623, 0.412604), (0.688199, 0.71808, 0.10365), (-0.364756, 0.218948, 0.904994)-10.1952, -22.07957, 13.70086
8given(0.892558, -0.433524, 0.124082), (-0.433101, -0.900785, -0.031787), (0.125552, -0.025368, -0.991763)-5.21574, -8.47989, 56.90971
9given(0.221479, -0.876646, 0.42713), (-0.87625, -0.371122, -0.307335), (0.427941, -0.306204, -0.850356)-3.52447, 15.86384, 42.67888
10given(-0.627305, -0.683735, 0.372819), (-0.685699, 0.257978, -0.680635), (0.369196, -0.682608, -0.630667)20.2933, 29.68507, 33.46141
11given(-0.999984, 0.005649, -0.000685), (0.003396, 0.495763, -0.868451), (-0.004567, -0.868439, -0.495774)47.79223, 21.65133, 36.38252
12given(-0.618869, 0.667687, -0.413757), (0.662594, 0.160843, -0.731505), (-0.421866, -0.726858, -0.541946)58.29715, -1.92961, 49.14059
13given(0.209144, 0.800947, -0.561019), (0.803146, -0.467981, -0.368714), (-0.557867, -0.373466, -0.741153)44.11512, -22.85497, 62.38254
14given(0.894622, 0.310315, -0.321491), (0.309943, -0.949235, -0.053748), (-0.321849, -0.05156, -0.945386)15.68684, -25.56694, 66.0715

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Components

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


Mass: 22702.602 Da / Num. of mol.: 14 / Mutation: N165D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: ATCC BAA-679 / EGD-e / Gene: clpP, lmo1138 / Plasmid: pDEST GATEWAY / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q8Y7Y1, endopeptidase Clp
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1181 / 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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 0.1 M Tris, 0.2 M MgCl2, 16% PEG3350 , pH 8.8, 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: Jul 28, 2012
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: 2.1→50 Å / Num. all: 177318 / Num. obs: 173949 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.4
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 3.5 / % possible all: 97.9

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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: 2.1→15 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.258 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24294 8698 5 %RANDOM
Rwork0.21886 ---
all0.221 165250 --
obs0.22007 165250 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.15 Å2
Baniso -1Baniso -2Baniso -3
1--1.73 Å20 Å20.1 Å2
2--1.38 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19040 0 0 1181 20221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01919544
X-RAY DIFFRACTIONr_angle_refined_deg0.9051.96226404
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.35852408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.51625.152924
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.003153668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.39915126
X-RAY DIFFRACTIONr_chiral_restr0.0590.23080
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214434
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 621 -
Rwork0.285 11745 -
obs--97.8 %

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