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- PDB-4mxi: ClpP Ser98dhA -

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Basic information

Entry
Database: PDB / ID: 4mxi
TitleClpP Ser98dhA
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / serine protease / ClpP / inhibition / complex disassembly / dehydroalanine
Function / homology
Function and homology information


endopeptidase Clp / endopeptidase Clp complex / protein quality control for misfolded or incompletely synthesized proteins / ATP-dependent peptidase activity / 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 speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGersch, M. / Kolb, R. / Alte, F. / Groll, M. / Sieber, S.A.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Disruption of Oligomerization and Dehydroalanine Formation as Mechanisms for ClpP Protease Inhibition.
Authors: Gersch, M. / Kolb, R. / Alte, F. / Groll, M. / Sieber, S.A.
History
DepositionSep 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Sep 20, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)150,6307
Polymers150,6307
Non-polymers00
Water7,512417
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)301,25914
Polymers301,25914
Non-polymers00
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area40310 Å2
ΔGint-264 kcal/mol
Surface area82900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.590, 121.590, 402.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.709765, 0.24549, -0.66028), (-0.48551, 0.849611, -0.206014), (0.510406, 0.466793, 0.722211)-3.66774, -17.58878, 24.16226
3given(0.018077, 0.078024, -0.996788), (-0.871265, 0.490294, 0.022578), (0.490481, 0.868058, 0.076843)-28.79942, -35.86079, 30.35469
4given(-0.529207, -0.40974, -0.743003), (-0.844983, 0.174931, 0.505374), (-0.077098, 0.895272, -0.438798)-53.42167, -39.79187, 12.1343
5given(-0.538497, -0.836192, -0.103943), (-0.427814, 0.165041, 0.888671), (-0.725945, 0.523015, -0.446609)-60.3382, -27.00587, -13.62388
6given(0.017776, -0.891265, 0.453134), (0.088259, 0.452835, 0.887215), (-0.995939, 0.024222, 0.086712)-43.74946, -6.09324, -30.77821
7given(0.700596, -0.512596, 0.496398), (0.260651, 0.831434, 0.490691), (-0.664249, -0.214389, 0.716108)-17.14678, 5.00339, -23.44411

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Components

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


Mass: 21518.516 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: NCTC 8325 / Gene: clpP, SAOUHSC_00790 / Plasmid: pET301 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2G036, endopeptidase Clp
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1 M Citric acid, 2.0 M (NH4)2SO4, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2013
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: 2.3→30 Å / Num. all: 79234 / Num. obs: 79191 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.6 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 23.34
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 4.85 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3V5E

3v5e


Resolution: 2.3→15 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.951 / SU B: 12.456 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22075 3960 5 %RANDOM
Rwork0.19618 ---
all0.199 79190 --
obs0.19741 75230 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.472 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20.91 Å2-0 Å2
2--0.91 Å2-0 Å2
3----2.96 Å2
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9217 0 0 417 9634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0199333
X-RAY DIFFRACTIONr_bond_other_d0.0010.029229
X-RAY DIFFRACTIONr_angle_refined_deg0.891.9712546
X-RAY DIFFRACTIONr_angle_other_deg0.956321231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.07651156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02225.448424
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.546151740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9641549
X-RAY DIFFRACTIONr_chiral_restr0.0540.21470
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210467
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021964
X-RAY DIFFRACTIONr_rigid_bond_restr1.489318561
X-RAY DIFFRACTIONr_sphericity_free30.9685155
X-RAY DIFFRACTIONr_sphericity_bonded5.69518708
LS refinement shellResolution: 2.3→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 280 -
Rwork0.23 5315 -
obs--100 %
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)
10.9643-0.10690.24940.415-0.27280.6885-0.0991-0.0591-0.04420.09860.09110.0741-0.12070.14430.0080.1754-0.04320.06290.12990.02540.0393-29.369940.553314.2128
21.7860.27310.44631.1179-0.07240.2453-0.1967-0.05430.1025-0.11080.12470.0614-0.04140.00930.0720.101-0.03890.01080.04780.00650.1234-51.193538.7261-2.1207
31.0496-0.0624-0.3041.20880.00640.684-0.0138-0.03440.0709-0.13250.05130.0332-0.05270.0032-0.03750.07-0.0295-0.0140.0211-0.01020.1577-74.478223.64670.8726
40.8589-0.0206-0.14250.6968-0.37131.09090.0096-0.0008-0.04560.10980.08080.1152-0.1405-0.0468-0.09050.17660.02280.03050.010.01310.1168-80.81976.30521.5297
50.34840.26540.18180.5159-0.03260.75290.0116-0.0043-0.0527-0.105-0.02630.0547-0.0898-0.00880.01480.20350.1073-0.01340.07540.02750.0712-66.23610.108144.1858
60.60170.3516-0.23220.4185-0.19970.4086-0.00480.0066-0.00180.0232-0.0160.00650.05530.1170.02080.1740.05620.03960.08950.05270.0593-40.99299.417851.9226
70.75090.3716-0.61630.974-0.11851.50550.0153-0.08280.03640.11010.07410.0750.04120.2816-0.08940.129-0.01090.04920.12930.00990.0442-24.598727.693738.6645
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 195
2X-RAY DIFFRACTION2B19 - 192
3X-RAY DIFFRACTION3C19 - 194
4X-RAY DIFFRACTION4D18 - 192
5X-RAY DIFFRACTION5E18 - 192
6X-RAY DIFFRACTION6F18 - 192
7X-RAY DIFFRACTION7G18 - 193

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