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- PDB-7qn2: Endothiapepsin in complex with compound TL00150 at room-temperatu... -

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Basic information

Entry
Database: PDB / ID: 7qn2
TitleEndothiapepsin in complex with compound TL00150 at room-temperature (temperature ramping up structure 12)
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)44,1208
Polymers43,2791
Non-polymers8417
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint16 kcal/mol
Surface area12630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.003, 74.106, 53.362
Angle α, β, γ (deg.)90.000, 109.601, 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.: 116 / 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: 37.88 %
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: 305 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→37.41 Å / Num. obs: 31391 / % possible obs: 98.61 % / Redundancy: 6.99 % / Biso Wilson estimate: 31.96 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.09 / Net I/σ(I): 12.5
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 6.59 % / Mean I/σ(I) obs: 1.13 / Num. unique obs: 3083 / CC1/2: 0.54 / Rrim(I) all: 1.37 / % possible all: 97.16

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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→37.41 Å / SU ML: 0.2443 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.3445
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1876 1632 5.2 %
Rwork0.1568 29754 -
obs0.1584 31386 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.47 Å2
Refinement stepCycle: LAST / Resolution: 1.79→37.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2379 0 52 116 2547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01622482
X-RAY DIFFRACTIONf_angle_d1.45693393
X-RAY DIFFRACTIONf_chiral_restr0.1064399
X-RAY DIFFRACTIONf_plane_restr0.0099426
X-RAY DIFFRACTIONf_dihedral_angle_d8.0517354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.840.36221160.3252475X-RAY DIFFRACTION97.15
1.84-1.90.26671280.26142442X-RAY DIFFRACTION97.64
1.9-1.970.33091250.26942448X-RAY DIFFRACTION98.06
1.97-2.050.27121310.20832449X-RAY DIFFRACTION97.95
2.05-2.140.20881260.17552477X-RAY DIFFRACTION98.49
2.14-2.260.2161400.16852432X-RAY DIFFRACTION98.36
2.26-2.40.22271350.17172503X-RAY DIFFRACTION98.69
2.4-2.580.21891250.16542493X-RAY DIFFRACTION99.05
2.58-2.840.20981340.16122499X-RAY DIFFRACTION99.13
2.84-3.250.18151710.16072475X-RAY DIFFRACTION99.4
3.25-4.10.16581490.13362508X-RAY DIFFRACTION99.74
4.1-37.410.13991520.12322553X-RAY DIFFRACTION99.78

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