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

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Basic information

Entry
Database: PDB / ID: 7qmg
TitleEndothiapepsin in complex with compound TL00150 at room-temperature (temperature ramping down structure 8)
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

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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)44,0427
Polymers43,2791
Non-polymers7636
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint15 kcal/mol
Surface area12640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.884, 74.017, 53.402
Angle α, β, γ (deg.)90.000, 109.519, 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.: 177 / 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: 1.97 Å3/Da / Density % sol: 37.72 %
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: 278 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→35.25 Å / Num. obs: 31685 / % possible obs: 99.8 % / Redundancy: 6.83 % / Biso Wilson estimate: 30.01 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.1 / Net I/σ(I): 11.39
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 6.38 % / Mean I/σ(I) obs: 1.16 / Num. unique obs: 3134 / CC1/2: 0.54 / Rrim(I) all: 1.49 / % possible all: 98.77

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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→35.25 Å / SU ML: 0.2676 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.3926
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2229 1571 4.96 %
Rwork0.1864 30106 -
obs0.1882 31677 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.39 Å2
Refinement stepCycle: LAST / Resolution: 1.79→35.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2379 0 48 178 2605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062479
X-RAY DIFFRACTIONf_angle_d0.82533390
X-RAY DIFFRACTIONf_chiral_restr0.0596399
X-RAY DIFFRACTIONf_plane_restr0.0054426
X-RAY DIFFRACTIONf_dihedral_angle_d7.5206354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.850.38681550.37642698X-RAY DIFFRACTION98.65
1.85-1.910.34041350.28192739X-RAY DIFFRACTION99.93
1.91-1.990.29371410.25562717X-RAY DIFFRACTION100
1.99-2.080.25181490.22252717X-RAY DIFFRACTION99.9
2.08-2.190.22071600.19162707X-RAY DIFFRACTION99.97
2.19-2.330.27571260.19752742X-RAY DIFFRACTION100
2.33-2.510.22241360.19222742X-RAY DIFFRACTION99.97
2.51-2.760.21141490.19222737X-RAY DIFFRACTION99.9
2.76-3.160.23491290.18922758X-RAY DIFFRACTION99.93
3.16-3.980.20911390.16722748X-RAY DIFFRACTION99.93
3.98-35.250.1851520.15612801X-RAY DIFFRACTION99.76

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