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- PDB-7qn0: Endothiapepsin in complex with compound TL00150 at room-temperatu... -

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Basic information

Entry
Database: PDB / ID: 7qn0
TitleEndothiapepsin in complex with compound TL00150 at room-temperature (temperature ramping up structure 10)
ComponentsEndothiapepsin
KeywordsHYDROLASE / Endopeptidase
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
1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / [4-(trifluoromethyl)phenyl]methanamine / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsHuang, C.Y. / Aumonier, S. / Wang, M.
Funding supportEuropean Union, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation182369European Union
Swiss National Science Foundation198290European Union
H2020 Marie Curie Actions of the European Commission884104European Union
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Probing ligand binding of endothiapepsin by `temperature-resolved' macromolecular crystallography.
Authors: Huang, C.Y. / Aumonier, S. / Engilberge, S. / Eris, D. / Smith, K.M.L. / Leonarski, F. / Wojdyla, J.A. / Beale, J.H. / Buntschu, D. / Pauluhn, A. / Sharpe, M.E. / Metz, A. / Olieric, V. / Wang, M.
History
DepositionDec 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 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
Revision 1.2Oct 16, 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: Endothiapepsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1208
Polymers43,2791
Non-polymers8417
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint16 kcal/mol
Surface area12690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.000, 74.129, 53.443
Angle α, β, γ (deg.)90.000, 109.676, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Endothiapepsin / Aspartate protease


Mass: 43278.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cryphonectria parasitica (chestnut blight fungus)
References: UniProt: P11838, endothiapepsin
#2: Chemical ChemComp-U1H / [4-(trifluoromethyl)phenyl]methanamine / 4-(Trifluoromethyl)benzylamine / p-trifluoromethylbenzylamine / 4-Aminomethylbenzotrifluoride


Mass: 175.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8F3N / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 1.98 Å3/Da / Density % sol: 37.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M ammonium acetate, 0.1 M sodium acetate pH 4.6, and 26 - 30% (v/v) PEG 4000

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Data collection

DiffractionMean temperature: 303 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 8, 2021
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→37.4 Å / Num. obs: 31443 / % possible obs: 98.54 % / Redundancy: 6.99 % / Biso Wilson estimate: 32.96 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.1 / Net I/σ(I): 12.27
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 6.57 % / Mean I/σ(I) obs: 0.95 / Num. unique obs: 3079 / CC1/2: 0.46 / Rrim(I) all: 1.73 / % possible all: 96.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RSV

6rsv


Resolution: 1.79→37.4 Å / SU ML: 0.2488 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.8642
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1943 1636 5.2 %
Rwork0.1662 29801 -
obs0.1677 31437 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.38 Å2
Refinement stepCycle: LAST / Resolution: 1.79→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2379 0 52 127 2558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00442486
X-RAY DIFFRACTIONf_angle_d0.7473400
X-RAY DIFFRACTIONf_chiral_restr0.0546400
X-RAY DIFFRACTIONf_plane_restr0.0043427
X-RAY DIFFRACTIONf_dihedral_angle_d7.7867356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.840.38661160.39662457X-RAY DIFFRACTION96.44
1.84-1.90.3291260.28542440X-RAY DIFFRACTION97.57
1.9-1.970.27931250.25952464X-RAY DIFFRACTION98.22
1.97-2.050.30331360.24152434X-RAY DIFFRACTION97.9
2.05-2.140.2071230.19932503X-RAY DIFFRACTION98.5
2.14-2.250.2371420.18732450X-RAY DIFFRACTION98.29
2.25-2.40.21581350.18352492X-RAY DIFFRACTION98.65
2.4-2.580.22811260.17792500X-RAY DIFFRACTION98.98
2.58-2.840.22841350.17212508X-RAY DIFFRACTION99.14
2.84-3.250.20081710.16822484X-RAY DIFFRACTION99.36
3.25-4.10.16581490.13882513X-RAY DIFFRACTION99.7
4.1-37.40.13961520.12692556X-RAY DIFFRACTION99.71

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