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- PDB-6n80: S. aureus ClpP bound to anti-4a -

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Basic information

Entry
Database: PDB / ID: 6n80
TitleS. aureus ClpP bound to anti-4a
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / ClpP
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
Chem-JT7 / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.96 Å
AuthorsLee, R.E. / Griffith, E.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI110578 United States
CitationJournal: J.Med.Chem. / Year: 2019
Title: De Novo Design of Boron-Based Peptidomimetics as Potent Inhibitors of Human ClpP in the Presence of Human ClpX.
Authors: Tan, J. / Grouleff, J.J. / Jitkova, Y. / Diaz, D.B. / Griffith, E.C. / Shao, W. / Bogdanchikova, A.F. / Poda, G. / Schimmer, A.D. / Lee, R.E. / Yudin, A.K.
History
DepositionNov 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
I: 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
S: ATP-dependent Clp protease proteolytic subunit
T: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,28628
Polymers316,50814
Non-polymers5,77814
Water28,4461579
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area47970 Å2
ΔGint-192 kcal/mol
Surface area86160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.332, 126.115, 145.461
Angle α, β, γ (deg.)90.000, 93.800, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 or (resid 6 and (name...
21(chain B and (resid 5 through 25 or (resid 26...
31(chain C and (resid 5 or (resid 6 and (name...
41(chain D and (resid 5 or (resid 6 and (name...
51(chain E and (resid 5 or (resid 6 and (name...
61(chain F and (resid 5 or (resid 6 and (name...
71(chain G and (resid 5 or (resid 6 and (name...
81(chain I and (resid 5 or (resid 6 and (name...
91(chain K and (resid 5 or (resid 6 and (name...
101(chain L and (resid 5 or (resid 6 and (name...
111(chain M and (resid 5 or (resid 6 and (name...
121(chain N and (resid 5 or (resid 6 and (name...
131(chain S and (resid 5 through 6 or resid 19...
141(chain T and (resid 5 or (resid 6 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPROPRO(chain A and (resid 5 or (resid 6 and (name...AA55
12THRTHRTHRTHR(chain A and (resid 5 or (resid 6 and (name...AA66
13ILEILEPROPRO(chain A and (resid 5 or (resid 6 and (name...AA4 - 1924 - 192
14ILEILEPROPRO(chain A and (resid 5 or (resid 6 and (name...AA4 - 1924 - 192
15ILEILEPROPRO(chain A and (resid 5 or (resid 6 and (name...AA4 - 1924 - 192
16ILEILEPROPRO(chain A and (resid 5 or (resid 6 and (name...AA4 - 1924 - 192
21PROPROLEULEU(chain B and (resid 5 through 25 or (resid 26...BB5 - 255 - 25
22LYSLYSLYSLYS(chain B and (resid 5 through 25 or (resid 26...BB2626
23PROPROGLUGLU(chain B and (resid 5 through 25 or (resid 26...BB5 - 1935 - 193
24PROPROGLUGLU(chain B and (resid 5 through 25 or (resid 26...BB5 - 1935 - 193
25PROPROGLUGLU(chain B and (resid 5 through 25 or (resid 26...BB5 - 1935 - 193
31PROPROPROPRO(chain C and (resid 5 or (resid 6 and (name...CC55
32THRTHRTHRTHR(chain C and (resid 5 or (resid 6 and (name...CC66
33ILEILETHRTHR(chain C and (resid 5 or (resid 6 and (name...CC4 - 1944 - 194
34ILEILETHRTHR(chain C and (resid 5 or (resid 6 and (name...CC4 - 1944 - 194
35ILEILETHRTHR(chain C and (resid 5 or (resid 6 and (name...CC4 - 1944 - 194
36ILEILETHRTHR(chain C and (resid 5 or (resid 6 and (name...CC4 - 1944 - 194
41PROPROPROPRO(chain D and (resid 5 or (resid 6 and (name...DD55
42THRTHRTHRTHR(chain D and (resid 5 or (resid 6 and (name...DD66
43ILEILEPROPRO(chain D and (resid 5 or (resid 6 and (name...DD4 - 1924 - 192
44ILEILEPROPRO(chain D and (resid 5 or (resid 6 and (name...DD4 - 1924 - 192
45ILEILEPROPRO(chain D and (resid 5 or (resid 6 and (name...DD4 - 1924 - 192
46ILEILEPROPRO(chain D and (resid 5 or (resid 6 and (name...DD4 - 1924 - 192
51PROPROPROPRO(chain E and (resid 5 or (resid 6 and (name...EE55
52THRTHRTHRTHR(chain E and (resid 5 or (resid 6 and (name...EE66
53ILEILEGLUGLU(chain E and (resid 5 or (resid 6 and (name...EE4 - 1934 - 193
54ILEILEGLUGLU(chain E and (resid 5 or (resid 6 and (name...EE4 - 1934 - 193
55ILEILEGLUGLU(chain E and (resid 5 or (resid 6 and (name...EE4 - 1934 - 193
56ILEILEGLUGLU(chain E and (resid 5 or (resid 6 and (name...EE4 - 1934 - 193
61PROPROPROPRO(chain F and (resid 5 or (resid 6 and (name...FF55
62THRTHRTHRTHR(chain F and (resid 5 or (resid 6 and (name...FF66
63ILEILEPROPRO(chain F and (resid 5 or (resid 6 and (name...FF4 - 1924 - 192
64ILEILEPROPRO(chain F and (resid 5 or (resid 6 and (name...FF4 - 1924 - 192
65ILEILEPROPRO(chain F and (resid 5 or (resid 6 and (name...FF4 - 1924 - 192
66ILEILEPROPRO(chain F and (resid 5 or (resid 6 and (name...FF4 - 1924 - 192
71PROPROPROPRO(chain G and (resid 5 or (resid 6 and (name...GG55
72THRTHRTHRTHR(chain G and (resid 5 or (resid 6 and (name...GG66
73ILEILEPROPRO(chain G and (resid 5 or (resid 6 and (name...GG4 - 1924 - 192
74ILEILEPROPRO(chain G and (resid 5 or (resid 6 and (name...GG4 - 1924 - 192
75ILEILEPROPRO(chain G and (resid 5 or (resid 6 and (name...GG4 - 1924 - 192
76ILEILEPROPRO(chain G and (resid 5 or (resid 6 and (name...GG4 - 1924 - 192
81PROPROPROPRO(chain I and (resid 5 or (resid 6 and (name...IH55
82THRTHRTHRTHR(chain I and (resid 5 or (resid 6 and (name...IH66
83ILEILEGLUGLU(chain I and (resid 5 or (resid 6 and (name...IH4 - 1934 - 193
84ILEILEGLUGLU(chain I and (resid 5 or (resid 6 and (name...IH4 - 1934 - 193
85ILEILEGLUGLU(chain I and (resid 5 or (resid 6 and (name...IH4 - 1934 - 193
86ILEILEGLUGLU(chain I and (resid 5 or (resid 6 and (name...IH4 - 1934 - 193
91PROPROPROPRO(chain K and (resid 5 or (resid 6 and (name...KI55
92THRTHRTHRTHR(chain K and (resid 5 or (resid 6 and (name...KI66
93ILEILEPROPRO(chain K and (resid 5 or (resid 6 and (name...KI4 - 1924 - 192
94ILEILEPROPRO(chain K and (resid 5 or (resid 6 and (name...KI4 - 1924 - 192
95ILEILEPROPRO(chain K and (resid 5 or (resid 6 and (name...KI4 - 1924 - 192
96ILEILEPROPRO(chain K and (resid 5 or (resid 6 and (name...KI4 - 1924 - 192
101PROPROPROPRO(chain L and (resid 5 or (resid 6 and (name...LJ55
102THRTHRTHRTHR(chain L and (resid 5 or (resid 6 and (name...LJ66
103ILEILEPROPRO(chain L and (resid 5 or (resid 6 and (name...LJ4 - 1924 - 192
104ILEILEPROPRO(chain L and (resid 5 or (resid 6 and (name...LJ4 - 1924 - 192
105ILEILEPROPRO(chain L and (resid 5 or (resid 6 and (name...LJ4 - 1924 - 192
106ILEILEPROPRO(chain L and (resid 5 or (resid 6 and (name...LJ4 - 1924 - 192
111PROPROPROPRO(chain M and (resid 5 or (resid 6 and (name...MK55
112THRTHRTHRTHR(chain M and (resid 5 or (resid 6 and (name...MK66
113ILEILEGLUGLU(chain M and (resid 5 or (resid 6 and (name...MK4 - 1934 - 193
114ILEILEGLUGLU(chain M and (resid 5 or (resid 6 and (name...MK4 - 1934 - 193
115ILEILEGLUGLU(chain M and (resid 5 or (resid 6 and (name...MK4 - 1934 - 193
116ILEILEGLUGLU(chain M and (resid 5 or (resid 6 and (name...MK4 - 1934 - 193
121PROPROPROPRO(chain N and (resid 5 or (resid 6 and (name...NL55
122THRTHRTHRTHR(chain N and (resid 5 or (resid 6 and (name...NL66
123ILEILEGLUGLU(chain N and (resid 5 or (resid 6 and (name...NL4 - 1934 - 193
124ILEILEGLUGLU(chain N and (resid 5 or (resid 6 and (name...NL4 - 1934 - 193
125ILEILEGLUGLU(chain N and (resid 5 or (resid 6 and (name...NL4 - 1934 - 193
126ILEILEGLUGLU(chain N and (resid 5 or (resid 6 and (name...NL4 - 1934 - 193
131PROPROTHRTHR(chain S and (resid 5 through 6 or resid 19...SM5 - 65 - 6
132ASPASPSERSER(chain S and (resid 5 through 6 or resid 19...SM19 - 2219 - 22
133ILEILEPROPRO(chain S and (resid 5 through 6 or resid 19...SM4 - 1924 - 192
134ILEILEPROPRO(chain S and (resid 5 through 6 or resid 19...SM4 - 1924 - 192
135ILEILEPROPRO(chain S and (resid 5 through 6 or resid 19...SM4 - 1924 - 192
136ILEILEPROPRO(chain S and (resid 5 through 6 or resid 19...SM4 - 1924 - 192
137ILEILEPROPRO(chain S and (resid 5 through 6 or resid 19...SM4 - 1924 - 192
138ILEILEPROPRO(chain S and (resid 5 through 6 or resid 19...SM4 - 1924 - 192
139ILEILEPROPRO(chain S and (resid 5 through 6 or resid 19...SM4 - 1924 - 192
141PROPROPROPRO(chain T and (resid 5 or (resid 6 and (name...TN55
142THRTHRTHRTHR(chain T and (resid 5 or (resid 6 and (name...TN66
143ILEILEPROPRO(chain T and (resid 5 or (resid 6 and (name...TN4 - 1924 - 192
144ILEILEPROPRO(chain T and (resid 5 or (resid 6 and (name...TN4 - 1924 - 192
145ILEILEPROPRO(chain T and (resid 5 or (resid 6 and (name...TN4 - 1924 - 192
146ILEILEPROPRO(chain T and (resid 5 or (resid 6 and (name...TN4 - 1924 - 192

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Components

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


Mass: 22607.686 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / Gene: clpP, SAOUHSC_00790 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2G036, endopeptidase Clp
#2: Chemical
ChemComp-JT7 / N-[(1R)-1-borono-3-methylbutyl]-N~2~-(2-chloro-4-methoxybenzene-1-carbonyl)-L-leucinamide


Mass: 412.716 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C19H30BClN2O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1579 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.65 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 4.5 / Details: 0.1 M NaOAc pH 4.5, 18-35% MPD, and 0.02 M CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 245159 / % possible obs: 99 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.076 / Rrim(I) all: 0.176 / Χ2: 1.054 / Net I/σ(I): 10 / Num. measured all: 1165384
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.96-1.993.10.809109200.3550.5030.9590.89288.7
1.99-2.033.60.735119630.6370.4210.850.92696.6
2.03-2.074.10.65121280.8210.3480.7390.91798.5
2.07-2.114.20.601123240.8550.3150.680.95899.4
2.11-2.164.30.527122550.890.2720.5940.97699.5
2.16-2.214.50.483122600.9020.2450.5431.01299.6
2.21-2.264.60.442123500.9120.220.4951.01799.6
2.26-2.324.70.413122770.9310.2010.461.05799.7
2.32-2.394.90.372123050.9390.1790.4141.04299.8
2.39-2.4750.351123060.9520.1660.3891.04199.8
2.47-2.5650.31123600.9570.1450.3441.05299.8
2.56-2.665.10.27123350.9610.1260.2991.0699.8
2.66-2.785.10.23124020.9650.1070.2541.06999.9
2.78-2.935.20.193123420.9730.090.2131.05599.9
2.93-3.115.20.165123910.9770.0770.1821.073100
3.11-3.355.20.144123780.9790.0670.1591.109100
3.35-3.695.20.126124100.980.0590.1391.164100
3.69-4.225.30.112124220.9840.0520.1241.14999.9
4.22-5.325.30.095124650.9860.0440.1050.989100
5.32-505.10.133125660.970.0630.1481.28199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.65 Å45.67 Å
Translation4.65 Å45.67 Å

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Processing

Software
NameVersionClassification
REFMACrefinement
HKL-2000data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→43.241 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2006 12121 4.96 %RANDOM
Rwork0.1712 ---
obs0.1726 245092 98.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.07 Å2 / Biso mean: 32.1731 Å2 / Biso min: 14.36 Å2
Refinement stepCycle: final / Resolution: 1.96→43.241 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19435 0 0 1579 21014
Biso mean---41.43 -
Num. residues----2524
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A11098X-RAY DIFFRACTION4.023TORSIONAL
12B11098X-RAY DIFFRACTION4.023TORSIONAL
13C11098X-RAY DIFFRACTION4.023TORSIONAL
14D11098X-RAY DIFFRACTION4.023TORSIONAL
15E11098X-RAY DIFFRACTION4.023TORSIONAL
16F11098X-RAY DIFFRACTION4.023TORSIONAL
17G11098X-RAY DIFFRACTION4.023TORSIONAL
18I11098X-RAY DIFFRACTION4.023TORSIONAL
19K11098X-RAY DIFFRACTION4.023TORSIONAL
110L11098X-RAY DIFFRACTION4.023TORSIONAL
111M11098X-RAY DIFFRACTION4.023TORSIONAL
112N11098X-RAY DIFFRACTION4.023TORSIONAL
113S11098X-RAY DIFFRACTION4.023TORSIONAL
114T11098X-RAY DIFFRACTION4.023TORSIONAL

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