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- PDB-3qwd: Crystal structure of ClpP from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 3qwd
TitleCrystal structure of ClpP from Staphylococcus aureus
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / caseinolytic protease / ClpP / serin-protease
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 / 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 NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGeiger, S.R. / Boettcher, T. / Sieber, S.A. / Cramer, P.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2011
Title: A Conformational Switch Underlies ClpP Protease Function.
Authors: Geiger, S.R. / Bottcher, T. / Sieber, S.A. / Cramer, P.
History
DepositionFeb 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)316,35021
Polymers316,10214
Non-polymers2487
Water5,278293
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
hetero molecules

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)316,35021
Polymers316,10214
Non-polymers2487
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_456x-1/2,-y+1/2,-z+11
Buried area53160 Å2
ΔGint-409 kcal/mol
Surface area86030 Å2
MethodPISA
2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,19311
Polymers158,0517
Non-polymers1424
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21990 Å2
ΔGint-184 kcal/mol
Surface area47120 Å2
MethodPISA
3
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)158,15710
Polymers158,0517
Non-polymers1063
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21780 Å2
ΔGint-177 kcal/mol
Surface area48300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.048, 177.974, 100.278
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 22578.680 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Strain: NCTC 8325 / Gene: clpP, SAOUHSC_00790 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q2G036, endopeptidase Clp
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.8 M ammonium sulfate and 100 mM sodium acetate pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2008
RadiationMonochromator: PILATUS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. obs: 179364 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 47.28 Å2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
BUSTER2.9.2refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→88.99 Å / Cor.coef. Fo:Fc: 0.9519 / Cor.coef. Fo:Fc free: 0.9407 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 8978 5.01 %RANDOM
Rwork0.2076 ---
all0.2086 ---
obs0.2086 179163 --
Displacement parametersBiso mean: 71.02 Å2
Baniso -1Baniso -2Baniso -3
1--4.32 Å20 Å20 Å2
2--6.2844 Å20 Å2
3----1.9644 Å2
Refine analyzeLuzzati coordinate error obs: 0.405 Å
Refinement stepCycle: LAST / Resolution: 2.1→88.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19927 0 7 293 20227
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01203962
X-RAY DIFFRACTIONt_angle_deg1.15275742
X-RAY DIFFRACTIONt_dihedral_angle_d073652
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion17.89
X-RAY DIFFRACTIONxx028855
X-RAY DIFFRACTIONt_ideal_dist_contact0233034
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2621 658 5.05 %
Rwork0.2617 12374 -
all0.2618 13032 -
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)
13.2467-1.31320.17443.91570.07271.0542-0.21620.12580.54270.49810.0899-0.3663-0.13370.04390.1263-0.0354-0.0514-0.0529-0.210.0856-0.010746.351832.992551.6806
23.61720.4147-0.39692.5895-0.22711.69690.02130.00780.54420.16850.1442-0.2247-0.00190.1327-0.1654-0.1109-0.085-0.152-0.3040.12460.30471.298742.549249.7041
32.13050.4059-0.63494.1264-1.13471.24120.0572-0.0449-0.07680.09430.1526-0.0745-0.0611-0.1852-0.2098-0.28450.0156-0.152-0.3040.06680.30479.421667.210343.8871
42.6367-0.1105-0.46622.7502-0.5221.24830.01560.002-0.04780.08720.0451-0.3384-0.0625-0.1778-0.0607-0.20310.0131-0.141-0.20930.00320.28563.62889.009137.7094
53.57070.83610.86913.0185-0.28951.6181-0.0276-0.0381-0.02260.01740.05260.04370.067-0.2082-0.0251-0.10190.0206-0.0412-0.1574-0.03220.007337.063190.92136.8385
62.23260.88470.94065.6465-0.2191.521-0.0055-0.195-0.13030.54420.08150.54420.0579-0.2076-0.076-0.18230.00360.1017-0.22870.0320.130818.223171.434741.3437
72.0448-0.53510.35955.6009-0.18210.8276-0.08870.03270.04570.54420.13290.0642-0.0877-0.018-0.0442-0.10010.01340.152-0.24330.07040.089722.931345.710248.3247
81.7402-0.72670.21963.3346-0.20382.05220.0705-0.12150.08340.46090.0226-0.4971-0.3241-0.0301-0.0931-0.0352-0.0473-0.152-0.1997-0.0369-0.0032156.11658.388489.2022
92.03680.11870.19912.2194-0.34552.06440.10980.0087-0.11710.31650.0080.1638-0.0707-0.1249-0.11770.0916-0.00840.013-0.1789-0.0565-0.069129.51565.270886.7751
102.4711.490.92792.0407-0.09281.5750.0433-0.36740.01030.42860.09730.4557-0.1826-0.3338-0.1405-0.06430.07430.152-0.19430.01230.1371107.54849.100291.0453
112.0467-0.015-0.20863.5475-0.19321.07610.2057-0.090.04250.5442-0.10050.03520.1111-0.1342-0.1052-0.0330.0470.152-0.22290.03390.0909106.65622.814897.9483
122.734-0.26530.12614.04520.46781.65170.14370.02770.42260.5442-0.0091-0.2547-0.040.0477-0.13460.10570.01060.0524-0.2180.0996-0.1185127.7346.0047101.718
133.52831.175-0.27924.3031-0.08521.41420.1697-0.1385-0.03720.5442-0.0562-0.5442-0.13990.2193-0.1135-0.1273-0.0022-0.152-0.27960.13320.0964154.20811.4227100.057
142.6227-0.15020.30853.1791-0.31351.86840.1349-0.3168-0.25620.5442-0.0941-0.5442-0.47070.3654-0.0408-0.1474-0.1011-0.152-0.25510.00490.1789166.59934.82993.946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|*}A3 - 194
2X-RAY DIFFRACTION2{B|*}B3 - 194
3X-RAY DIFFRACTION3{C|*}C3 - 197
4X-RAY DIFFRACTION4{D|*}D3 - 192
5X-RAY DIFFRACTION5{E|*}E3 - 195
6X-RAY DIFFRACTION6{F|*}F4 - 193
7X-RAY DIFFRACTION7{G|*}G3 - 193
8X-RAY DIFFRACTION8{H|*}H3 - 202
9X-RAY DIFFRACTION9{I|*}I3 - 197
10X-RAY DIFFRACTION10{J|*}J3 - 194
11X-RAY DIFFRACTION11{K|*}K3 - 193
12X-RAY DIFFRACTION12{L|*}L3 - 193
13X-RAY DIFFRACTION13{M|*}M3 - 194
14X-RAY DIFFRACTION14{N|*}N3 - 193

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