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- PDB-7bkv: Endothiapepsin structure obtained at 100K with fragment AC39729 bound -

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Basic information

Entry
Database: PDB / ID: 7bkv
TitleEndothiapepsin structure obtained at 100K with fragment AC39729 bound
ComponentsEndothiapepsin
KeywordsHYDROLASE / FBDD / inhibitor
Function / homology
Function and homology information


endothiapepsin / aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Aspergillopepsin-like catalytic domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / 5-fluoranylpyridin-2-amine / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.24 Å
AuthorsEngilberge, S. / Huang, C.-Y. / Smith, K.M.L. / Eris, D. / Marsh, M. / Wang, M. / Wojdyla, J.A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation200021_182369 Switzerland
CitationJournal: To Be Published
Title: Endothiapepsin structure obtained at 100K with fragment AC39729 bound
Authors: Engilberge, S. / Huang, C.-Y. / Smith, K.M.L. / Eris, D. / Wojdyla, J.A. / Olieric, V. / Leonarski, F. / Sharpe, M. / Wang, M.
History
DepositionJan 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endothiapepsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,06727
Polymers33,8141
Non-polymers2,25426
Water9,926551
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint39 kcal/mol
Surface area13340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.295, 73.492, 52.830
Angle α, β, γ (deg.)90.000, 109.930, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Endothiapepsin / Aspartate protease


Mass: 33813.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cryphonectria parasitica (chestnut blight fungus)
References: UniProt: P11838, endothiapepsin

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Non-polymers , 5 types, 577 molecules

#2: Chemical ChemComp-U1Q / 5-fluoranylpyridin-2-amine


Mass: 112.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5FN2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 551 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.44 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 100 mM ammonium acetate, 100 mM sodium acetate pH 4.6 and 26 to 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.24→42.58 Å / Num. obs: 70862 / % possible obs: 77.09 % / Redundancy: 6.3 % / CC1/2: 0.99 / Rpim(I) all: 0.0209 / Net I/σ(I): 19.22
Reflection shellResolution: 1.24→1.28 Å / Mean I/σ(I) obs: 1.51 / Num. unique obs: 4490 / CC1/2: 0.72 / Rpim(I) all: 0.4482

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RSV

6rsv


Resolution: 1.24→42.58 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1619 3525 4.97 %
Rwork0.1413 67337 -
obs0.1423 70862 76.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.95 Å2 / Biso mean: 17.9482 Å2 / Biso min: 1.52 Å2
Refinement stepCycle: final / Resolution: 1.24→42.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2380 0 115 553 3048
Biso mean--36.12 30.32 -
Num. residues----330
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.24-1.260.3474110.26643043159
1.26-1.270.3172310.290252055115
1.27-1.290.2902420.259776981122
1.29-1.310.3172630.25151048111130
1.31-1.330.285690.22981260132936
1.33-1.360.2682930.22061574166746
1.36-1.380.2349950.20511930202555
1.38-1.410.23021120.20042286239865
1.41-1.440.22611400.1872605274575
1.44-1.470.19261590.18092939309884
1.47-1.50.18211670.17113243341093
1.5-1.540.19461830.16383446362998
1.54-1.580.16351790.15473466364599
1.58-1.630.18591840.148735363720100
1.63-1.680.1982030.14923442364599
1.68-1.740.18531920.14173480367299
1.74-1.810.17551750.1423457363299
1.81-1.890.1551530.13953492364599
1.89-1.990.14991850.127434713656100
1.99-2.120.13651710.124935173688100
2.12-2.280.14331730.120935213694100
2.28-2.510.15391820.133498368099
2.51-2.870.14371790.12973464364398
2.87-3.620.16071940.129935073701100
3.62-42.580.14351900.14363562375299

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