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- PDB-6uqd: Co-complex of S. pyogenes 10782 streptopain bound with a SuFEx-ba... -

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Basic information

Entry
Database: PDB / ID: 6uqd
TitleCo-complex of S. pyogenes 10782 streptopain bound with a SuFEx-based optimized small molecule inhibitor
ComponentsStreptopain
KeywordsHYDROLASE/HYDROLASE INHIBITOR / speb / streptopain / inhibitor / nitrile / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


streptopain / symbiont-mediated suppression of host autophagy / symbiont-induced defense-related programmed cell death / symbiont-mediated evasion of host immune response / host cell cytosol / cysteine-type peptidase activity / toxin activity / host extracellular space / cysteine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Spi protease inhibitor / Spi protease inhibitor / Peptidase C10, streptopain / Peptidase C10, streptopain superfmaily / Peptidase C10 family / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Chem-QF4 / Streptopain
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsWolan, D.W. / Woehl, J.L. / Kitamura, S.
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Sulfur(VI) Fluoride Exchange (SuFEx)-Enabled High-Throughput Medicinal Chemistry.
Authors: Kitamura, S. / Zheng, Q. / Woehl, J.L. / Solania, A. / Chen, E. / Dillon, N. / Hull, M.V. / Kotaniguchi, M. / Cappiello, J.R. / Kitamura, S. / Nizet, V. / Sharpless, K.B. / Wolan, D.W.
History
DepositionOct 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
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: Streptopain
B: Streptopain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0794
Polymers83,1042
Non-polymers9752
Water6,936385
1
A: Streptopain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0392
Polymers41,5521
Non-polymers4881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Streptopain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0392
Polymers41,5521
Non-polymers4881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.624, 115.516, 50.265
Angle α, β, γ (deg.)90.000, 112.580, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Streptopain / Exotoxin type B / SPE B / Streptococcal cysteine proteinase / Streptococcus peptidase A / SPP


Mass: 41551.945 Da / Num. of mol.: 2 / Fragment: UNP residues 28-398
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: speB / Production host: Escherichia coli (E. coli) / References: UniProt: P0C0J0, streptopain
#2: Chemical ChemComp-QF4 / benzyl [(1S)-2-(3-{[(4-carbamoylpiperidin-1-yl)(fluoro)oxo-lambda~6~-sulfanylidene]amino}phenyl)-1-cyanoethyl]carbamate


Mass: 487.547 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H26FN5O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.47 Å3/Da / Density % sol: 16.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1-0.15 M sodium nitrate, 22-27% PEG3350 / PH range: 6.8-7.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.02→43.07 Å / Num. obs: 29212 / % possible obs: 94.5 % / Redundancy: 2.6 % / Biso Wilson estimate: 10.6 Å2 / Rmerge(I) obs: 0.182 / Net I/σ(I): 7.2
Reflection shellResolution: 2.02→2.05 Å / Rmerge(I) obs: 0.544 / Num. unique obs: 1464 / % possible all: 93.1

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4RKX

4rkx


Resolution: 2.02→43.07 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.61
RfactorNum. reflection% reflection
Rfree0.257 1384 4.74 %
Rwork0.215 27797 -
obs0.217 29181 93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 64.63 Å2 / Biso mean: 14.77 Å2 / Biso min: 2.33 Å2
Refinement stepCycle: final / Resolution: 2.02→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3853 0 68 385 4306
Biso mean--32.08 23.84 -
Num. residues----501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0224-2.09470.34091070.27252364247178
2.0947-2.17860.29181470.25192709285692
2.1786-2.27770.27411600.2362824298495
2.2777-2.39780.28161420.22552877301997
2.3978-2.5480.28991410.22522897303897
2.548-2.74470.27141360.22252832296895
2.7447-3.02090.31941030.22282806290993
3.0209-3.45790.24461480.19882897304597
3.4579-4.35590.20031560.17892765292193
4.3559-43.0660.22051440.19562826297093
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)
11.22730.08560.80080.41870.11620.53070.02960.3792-0.0225-0.09560.0058-0.12240.10040.14330.16530.1070.02820.00870.1041-0.01330.08644.6073-23.441415.4609
20.5983-0.0271-0.01810.8123-0.19880.70510.0345-0.1743-0.04620.0007-0.03690.1678-0.0298-0.0069-0.03180.0448-0.0136-0.00760.04270.01040.0548-10.6729-14.14931.8187
30.8808-0.3389-0.25450.1940.03140.68770.0430.0561-0.02690.0083-0.141-0.08370.09140.02850.00010.08-0.0019-0.00790.08080.01660.07020.8908-20.799933.5167
40.1248-0.09540.0160.20330.07611.1863-0.06820.05590.0803-0.0740.04310.0115-0.2137-0.04710.32780.063-0.0026-0.03060.0510.01140.0681-4.4909-5.91920.3618
50.1786-0.15890.12240.79990.18640.9508-0.0150.04430.1174-0.1039-0.0587-0.0983-0.06970.092-0.03060.07490.00240.0230.08370.00760.0664-0.1914-11.55138.6762
61.9044-0.38780.40810.6485-0.10990.567-0.01820.1777-0.06890.0434-0.04750.0310.29410.0815-0.1790.12790.0145-0.02080.0157-0.00270.033-4.3942-20.95749.2379
71.87730.53110.32690.99920.17611.6828-0.065-0.0277-0.1895-0.01880.006-0.15090.1793-0.2184-0.84450.12430.0442-0.01180.0285-0.00050.0497-7.4141-14.096112.0481
81.24940.2499-0.29311.21340.18880.99150.04870.08080.0297-0.09190.01130.0961-0.16370.01410.06490.0620.019-0.02580.03460.00720.03844.89618.21250.1412
90.6112-0.1985-0.00350.5847-0.20170.5583-0.04360.1119-0.0994-0.07330.0387-0.00230.23410.10510.0990.1119-0.02490.00990.114-0.04440.0444.00818.5136-13.0913
100.8575-0.22190.07820.86580.27280.51190.08980.16860.1030.0307-0.0478-0.3548-0.00660.09810.42070.03570.0133-0.00280.0745-0.00170.090716.159323.47092.5833
110.65070.58560.09441.20140.01330.1454-0.1520.1774-0.035-0.10550.1395-0.2355-0.02220.03140.01230.0552-0.0015-0.00020.06130.00080.1112.017818.3278-2.7333
120.52940.0116-0.32880.54370.15890.8531-0.0806-0.0696-0.16340.0011-0.05320.00530.2137-0.0974-0.89020.0888-0.0440.0080.07260.05090.04921.59826.15775.9651
131.4218-0.282-0.0660.8276-0.2110.85630.1754-0.17520.04650.10230.11820.24360.0017-0.24871.42480.0875-0.01920.03710.11090.06880.0942-4.672310.740722.2823
142.56990.10011.46790.75570.28331.7953-0.0663-0.1721-0.0101-0.1210.0363-0.0223-0.2546-0.0986-0.04140.05250.0280.0127-0.03680.02160.0411-3.836715.330510.6632
150.50480.246-0.19070.92170.05830.60280.0581-0.03410.05930.0924-0.02420.1941-0.007-0.0781-0.02390.031-0.00970.01030.0612-0.01440.1127-7.63919.105511.9082
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 146 THROUGH 161 )A0
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 162 THROUGH 237 )A0
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 238 THROUGH 272 )A0
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 273 THROUGH 311 )A0
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 312 THROUGH 337 )A0
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 338 THROUGH 372 )A0
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 373 THROUGH 398 )A0
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 146 THROUGH 217 )B0
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 218 THROUGH 237 )B0
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 238 THROUGH 254 )B0
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 255 THROUGH 272 )B0
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 273 THROUGH 311 )B0
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 312 THROUGH 324 )B0
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 325 THROUGH 347 )B0
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 348 THROUGH 399 )B0

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