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- PDB-6ukd: Co-complex of S. pyogenes 10782 streptopain bound with a nitrile-... -

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Basic information

Entry
Database: PDB / ID: 6ukd
TitleCo-complex of S. pyogenes 10782 streptopain bound with a nitrile-based specific covalent inhibitor
ComponentsStreptopain
KeywordsHYDROLASE/HYDROLASE INHIBITOR / speb / streptopain / inhibitor / nitrile / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


: / streptopain / symbiont-induced defense-related programmed cell death / symbiont-mediated suppression of host autophagy / symbiont-mediated evasion of host immune response / host cell cytosol / cysteine-type peptidase activity / toxin activity / host extracellular space / cysteine-type endopeptidase activity ...: / streptopain / symbiont-induced defense-related programmed cell death / symbiont-mediated suppression of host autophagy / 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
NITRATE ION / Chem-Q9D / Streptopain
Similarity search - Component
Biological speciesStreptococcus pyogenes ATCC 10782 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.589 Å
AuthorsWolan, D.W. / Woehl, J.L. / Kitamura, S.
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: An Irreversible Inhibitor to Probe the Role ofStreptococcus pyogenesCysteine Protease SpeB in Evasion of Host Complement Defenses.
Authors: Woehl, J.L. / Kitamura, S. / Dillon, N. / Han, Z. / Edgar, L.J. / Nizet, V. / Wolan, D.W.
History
DepositionOct 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Streptopain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0184
Polymers41,5521
Non-polymers4663
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint2 kcal/mol
Surface area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.273, 50.398, 114.497
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-771-

HOH

21A-841-

HOH

31A-854-

HOH

41A-908-

HOH

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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.: 1 / Fragment: UNP residues 28-398
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes ATCC 10782 (bacteria)
Gene: speB / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / References: UniProt: P0C0J0, streptopain
#2: Chemical ChemComp-Q9D / benzyl [(2S)-1-(3-nitrophenyl)-3-oxobutan-2-yl]carbamate


Mass: 342.346 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.87 Å3/Da / Density % sol: 34.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M sodium nitrate, 33% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.58→46.13 Å / Num. obs: 29409 / % possible obs: 98.3 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.045 / Rrim(I) all: 0.115 / Net I/σ(I): 17.4
Reflection shellResolution: 1.59→1.66 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2644 / CC1/2: 0.826 / Rpim(I) all: 0.222 / Rrim(I) all: 0.477 / % possible all: 90

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Processing

Software
NameVersionClassification
PHENIX1.14refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4D8B

4d8b


Resolution: 1.589→46.127 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.19
RfactorNum. reflection% reflection
Rfree0.189 1408 4.79 %
Rwork0.1529 --
obs0.1545 29406 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 62.08 Å2 / Biso mean: 15.5128 Å2 / Biso min: 6.33 Å2
Refinement stepCycle: final / Resolution: 1.589→46.127 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1974 0 33 317 2324
Biso mean--25.17 27.37 -
Num. residues----257
LS refinement shellResolution: 1.59→1.65 Å / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.207
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)
10.71370.1411-0.02830.25050.07430.4186-0.0243-0.0378-0.01140.03020.07480.01980.0268-0.040.01170.0714-0.01250.00120.0748-0.00430.0545-15.6601-11.367120.7099
20.2505-0.1512-0.17340.5957-0.02440.90990.00860.01650.0101-0.02750.019-0.0004-0.06410.0807-0.00040.071-0.0230.01230.0654-0.01480.0863-9.9312-4.656113.3729
30.9521-0.27390.07670.267-0.14990.09340.0322-0.05110.00320.02680.0814-0.1276-0.01030.0529-0.02240.0897-0.00540.00320.0703-0.00310.0875-8.3766-5.54417.9642
40.66170.2779-0.14810.90030.13350.6599-0.01740.0159-0.0929-0.04490.0367-0.00230.0668-0.01980.02570.0609-0.00520.00150.0506-0.0060.0508-15.9413-23.705810.9405
50.44760.36470.44830.99840.08741.01040.006-0.01770.0470.04790.06460.02010.0422-0.10580.01220.07590.00070.00520.0564-0.00170.0659-20.1963-24.627617.9578
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 146 through 204 )A146 - 204
2X-RAY DIFFRACTION2chain 'A' and (resid 205 through 254 )A205 - 254
3X-RAY DIFFRACTION3chain 'A' and (resid 255 through 272 )A255 - 272
4X-RAY DIFFRACTION4chain 'A' and (resid 273 through 356 )A273 - 356
5X-RAY DIFFRACTION5chain 'A' and (resid 357 through 402 )A357 - 402

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