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- PDB-5dl1: ClpP from Staphylococcus aureus in complex with AV145 -

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Basic information

Entry
Database: PDB / ID: 5dl1
TitleClpP from Staphylococcus aureus in complex with AV145
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex / caseinolytic protease / allosteric regulation / binding analysis
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 / identical protein binding / 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
Chem-5C2 / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsVielberg, M.-T. / Groll, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB1035 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Reversible Inhibitors Arrest ClpP in a Defined Conformational State that Can Be Revoked by ClpX Association.
Authors: Pahl, A. / Lakemeyer, M. / Vielberg, M.T. / Hackl, M.W. / Vomacka, J. / Korotkov, V.S. / Stein, M.L. / Fetzer, C. / Lorenz-Baath, K. / Richter, K. / Waldmann, H. / Groll, M. / Sieber, S.A.
History
DepositionSep 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Oct 24, 2018Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / pdbx_validate_symm_contact / struct_conn
Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)306,65528
Polymers301,51114
Non-polymers5,14414
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.820, 97.750, 131.950
Angle α, β, γ (deg.)90.00, 95.49, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
12H
22I
32J
42K
52L
62M
72N

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 300
2111B1 - 300
3111C1 - 300
4111D1 - 300
5111E1 - 300
6111F1 - 300
7111G1 - 300
1121H1 - 300
2121I1 - 300
3121J1 - 300
4121K1 - 300
5121L1 - 300
6121M1 - 300
7121N1 - 300

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.80939, -0.539985, -0.230875), (0.573289, 0.641226, 0.510068), (-0.127386, -0.545202, 0.82857)-0.94318, -0.81654, -0.47923
3given(0.368236, -0.663598, -0.651183), (0.748272, -0.204162, 0.631194), (-0.551807, -0.719691, 0.421372)-1.21225, -2.15363, -1.36507
4given(-0.018531, -0.257456, -0.966112), (0.394383, -0.889812, 0.229558), (-0.918759, -0.376764, 0.118025)-1.04901, -3.27843, -1.54321
5given(0.793392, 0.5885, -0.155556), (-0.565262, 0.61748, -0.546989), (-0.225851, 0.521906, 0.82256)1.34592, -1.42974, 0.98888
6given(0.336767, 0.747693, -0.572314), (-0.667345, -0.239263, -0.705269), (-0.664258, 0.619442, 0.418394)1.27097, -3.40412, 1.07217
7given(-0.032465, 0.369485, -0.928669), (-0.239684, -0.904924, -0.351659), (-0.970308, 0.211171, 0.117938)0.19252, -4.36787, -0.53413
8given(1), (1), (1)
9given(0.805719, 0.573442, -0.14826), (-0.549653, 0.630641, -0.547881), (-0.220679, 0.522929, 0.823314)1.04413, -0.88179, 0.92897
10given(0.35358, 0.751144, -0.557463), (-0.660983, -0.221059, -0.717101), (-0.661878, 0.622026, 0.418332)0.84248, -2.00952, 0.99828
11given(-0.025122, 0.377298, -0.925751), (-0.250841, -0.898796, -0.359505), (-0.967702, 0.223184, 0.117222)-0.5403, -4.23933, -0.48753
12given(0.799272, -0.554543, -0.231615), (0.58268, 0.620725, 0.524581), (-0.147133, -0.55424, 0.819249)-1.0737, -0.57693, -1.00936
13given(0.353505, -0.661639, -0.661263), (0.754165, -0.216632, 0.619925), (-0.553417, -0.717847, 0.422404)-1.45433, -1.54582, -1.56928
14given(-0.029389, -0.243634, -0.969422), (0.38936, -0.896028, 0.213385), (-0.920617, -0.371183, 0.121194)-2.36632, -2.71699, -1.7307

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Components

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


Mass: 21536.531 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: clpP, SAB0722 / Plasmid: pET301 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q2YSF8, UniProt: Q2G036*PLUS, endopeptidase Clp
#2: Chemical
ChemComp-5C2 / 1-(propan-2-yl)-N-{[2-(thiophen-2-yl)-1,3-oxazol-4-yl]methyl}-1H-pyrazolo[3,4-b]pyridine-5-carboxamide


Mass: 367.425 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C18H17N5O2S

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 200 mM KNO3, 20% PEG3350

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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: Nov 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 56975 / % possible obs: 99.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.1
Reflection shellResolution: 3→3.1 Å / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

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Processing

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

3v5e


Resolution: 3→15 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.913 / SU B: 73.661 / SU ML: 0.564 / Cross valid method: THROUGHOUT / ESU R Free: 0.519 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27409 2849 5 %RANDOM
Rwork0.25162 ---
obs0.25273 54126 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 116.775 Å2
Baniso -1Baniso -2Baniso -3
1-6.55 Å20 Å211.28 Å2
2--1.82 Å2-0 Å2
3----9.28 Å2
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20342 0 364 0 20706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221000
X-RAY DIFFRACTIONr_bond_other_d0.0020.0220496
X-RAY DIFFRACTIONr_angle_refined_deg0.8931.99728378
X-RAY DIFFRACTIONr_angle_other_deg0.7343.00447138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.252604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.87125.455924
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.271153794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.32915112
X-RAY DIFFRACTIONr_chiral_restr0.0420.23276
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0223660
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024452
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.98341496
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded11.306541202
Refine LS restraints NCS

Number: 2943 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDRms dev position (Å)
11A6.36
12B7.85
13C6.22
14D6.09
15E6.81
16F6.65
17G6.61
21H6.34
22I7.57
23J6.34
24K5.69
25L7.88
26M7.42
27N7.05
LS refinement shellResolution: 3→3.075 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 203 -
Rwork0.37 3852 -
obs--99.85 %
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)
11.21960.4011-0.01150.9987-0.93211.0152-0.18920.2259-0.0133-0.14480.1485-0.05390.1499-0.16090.04070.3006-0.194-0.27150.4793-0.19460.6513-34.0061-19.8048-1.2794
21.7620.1856-1.44441.003-0.10532.64490.19510.0740.15810.03460.086-0.117-0.505-0.513-0.28120.33150.0629-0.29770.55040.0840.5744-37.54396.1116-2.7166
30.85970.03970.23291.34461.09881.38970.0162-0.33490.0222-0.1690.2615-0.0467-0.74440.2794-0.27771.0437-0.23890.01380.36180.00850.7796-25.332125.301710.2481
41.0123-0.91630.69531.81060.35441.98950.1344-0.12250.0478-0.0184-0.0791-0.2371-0.34420.3292-0.05530.6065-0.596-0.16330.875-0.08450.8332-6.148923.093928.0763
51.34270.41510.30171.229-0.04612.2842-0.25420.006-0.1920.16650.06860.18090.79350.35650.18560.57710.1768-0.09320.4104-0.11830.8386-17.1467-33.336113.6837
60.90940.31670.1180.67890.97521.8965-0.2643-0.1301-0.16750.21710.09960.16310.63540.82420.16470.42060.3271-0.17291.04880.01220.78620.6286-23.909230.7734
70.2636-0.3142-0.8223.1023-0.29493.1796-0.0336-0.22450.04690.1510.0638-0.07020.01820.8959-0.03020.2381-0.2231-0.38131.4379-0.090.84675.53421.175437.0976
81.67220.0082-0.19650.71310.94211.3715-0.0785-0.34360.08990.1830.1139-0.05490.35440.4259-0.03540.41440.2275-0.33950.60180.16380.5872-27.5962-21.330966.1185
90.80660.01130.37281.47410.281.02240.0304-0.03410.15280.02620.12440.1628-0.21120.66-0.15480.3818-0.1974-0.28430.7221-0.14160.5679-26.21674.774569.1238
101.72160.21270.35761.3564-1.10911.91050.09040.25660.0714-0.13930.01110.0332-0.4978-0.0722-0.10150.7833-0.0625-0.10090.3253-0.10580.668-40.385323.421856.9508
110.65570.83380.54891.87090.02811.2369-0.02140.1036-0.00330.05310.030.079-0.3434-0.1977-0.00860.56090.3231-0.10840.67990.0080.8398-59.487720.02238.9976
121.39690.3230.26910.82940.01283.1169-0.1676-0.1096-0.0840.024-0.062-0.0860.7057-0.00810.22970.6715-0.0441-0.15630.18460.07390.7108-43.1673-35.383550.253
130.2442-0.15630.560.9168-0.8372.717-0.04910.12830.0790.1298-0.0118-0.07880.5649-0.30340.06090.4839-0.3244-0.23180.6139-0.09680.7103-61.6234-27.009233.6068
140.210.2315-0.7061.95350.28173.04340.04250.22010.01480.12580.0068-0.0535-0.0941-0.8214-0.04930.15430.1254-0.33520.9932-0.00590.8433-68.9723-2.360628.7054
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 193
2X-RAY DIFFRACTION2B1 - 193
3X-RAY DIFFRACTION3C1 - 193
4X-RAY DIFFRACTION4D1 - 193
5X-RAY DIFFRACTION5E1 - 193
6X-RAY DIFFRACTION6F1 - 193
7X-RAY DIFFRACTION7G1 - 193
8X-RAY DIFFRACTION8H1 - 193
9X-RAY DIFFRACTION9I1 - 193
10X-RAY DIFFRACTION10J1 - 193
11X-RAY DIFFRACTION11K1 - 193
12X-RAY DIFFRACTION12L1 - 193
13X-RAY DIFFRACTION13M1 - 193
14X-RAY DIFFRACTION14N1 - 193

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