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

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Basic information

Entry
Database: PDB / ID: 7qmf
TitleEndothiapepsin in complex with compound TL00150 at room-temperature (temperature ramping down structure 7)
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
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint15 kcal/mol
Surface area12680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.916, 74.073, 53.476
Angle α, β, γ (deg.)90.000, 109.537, 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.: 167 / 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: 37.89 %
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: 281 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→37.36 Å / Num. obs: 31662 / % possible obs: 99.65 % / Redundancy: 6.38 % / Biso Wilson estimate: 28.64 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.15 / Net I/σ(I): 9.43
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.04 / Num. unique obs: 3116 / CC1/2: 0.51 / Rrim(I) all: 1.75 / % possible all: 98.39

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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→37.36 Å / SU ML: 0.2411 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.092
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2173 1567 4.95 %
Rwork0.1817 30080 -
obs0.1834 31647 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.3 Å2
Refinement stepCycle: LAST / Resolution: 1.79→37.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2379 0 48 169 2596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00482479
X-RAY DIFFRACTIONf_angle_d0.78143390
X-RAY DIFFRACTIONf_chiral_restr0.0572399
X-RAY DIFFRACTIONf_plane_restr0.0047426
X-RAY DIFFRACTIONf_dihedral_angle_d7.755354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.850.34491540.35032685X-RAY DIFFRACTION98.24
1.85-1.920.33851350.26422741X-RAY DIFFRACTION99.97
1.92-1.990.25251420.24082729X-RAY DIFFRACTION99.93
1.99-2.080.23341460.20432713X-RAY DIFFRACTION99.9
2.08-2.190.22081620.17912707X-RAY DIFFRACTION100
2.19-2.330.24791270.18222740X-RAY DIFFRACTION99.86
2.33-2.510.21961360.18342738X-RAY DIFFRACTION99.76
2.51-2.760.21361480.18222733X-RAY DIFFRACTION99.83
2.76-3.160.22381270.18592756X-RAY DIFFRACTION99.65
3.16-3.980.20911380.16382741X-RAY DIFFRACTION99.62
3.98-37.360.18361520.15932797X-RAY DIFFRACTION99.53

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