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

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Basic information

Entry
Database: PDB / ID: 7qmo
TitleEndothiapepsin in complex with compound TL00150 at room-temperature (temperature ramping down structure 16)
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 23, 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)44,0427
Polymers43,2791
Non-polymers7636
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint15 kcal/mol
Surface area12570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.731, 73.906, 53.387
Angle α, β, γ (deg.)90.000, 109.720, 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.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 1.96 Å3/Da / Density % sol: 37.32 %
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: 266 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→37.02 Å / Num. obs: 31549 / % possible obs: 99.86 % / Redundancy: 6.79 % / Biso Wilson estimate: 26.35 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.23 / Net I/σ(I): 7.89
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 6.38 % / Mean I/σ(I) obs: 0.92 / Num. unique obs: 3144 / CC1/2: 0.63 / Rrim(I) all: 1.69 / % possible all: 99.87

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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→37.02 Å / SU ML: 0.2032 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.8333
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2209 1569 4.96 %
Rwork0.1947 30071 -
obs0.1959 31532 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.2 Å2
Refinement stepCycle: LAST / Resolution: 1.79→37.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2379 0 48 204 2631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212479
X-RAY DIFFRACTIONf_angle_d0.55283390
X-RAY DIFFRACTIONf_chiral_restr0.0438399
X-RAY DIFFRACTIONf_plane_restr0.0029426
X-RAY DIFFRACTIONf_dihedral_angle_d7.1354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.850.3361580.33342712X-RAY DIFFRACTION99.14
1.85-1.910.33971330.31652731X-RAY DIFFRACTION99.83
1.91-1.990.28711430.26652726X-RAY DIFFRACTION99.93
1.99-2.080.25231490.24852706X-RAY DIFFRACTION99.83
2.08-2.190.26251540.23842689X-RAY DIFFRACTION99.89
2.19-2.320.27081280.22792741X-RAY DIFFRACTION99.9
2.33-2.50.24531360.21172734X-RAY DIFFRACTION99.83
2.5-2.760.21181490.19742735X-RAY DIFFRACTION99.97
2.76-3.150.23191280.1862759X-RAY DIFFRACTION99.93
3.16-3.970.17221390.16122739X-RAY DIFFRACTION99.79
3.98-37.020.18421520.1522799X-RAY DIFFRACTION99.9

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