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- PDB-7qlz: Endothiapepsin in 5% DMSO at 298 K -

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Basic information

Entry
Database: PDB / ID: 7qlz
TitleEndothiapepsin in 5% DMSO at 298 K
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
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 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endothiapepsin


Theoretical massNumber of molelcules
Total (without water)43,2791
Polymers43,2791
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13090 Å2
Unit cell
Length a, b, c (Å)45.974, 74.116, 53.372
Angle α, β, γ (deg.)90.000, 109.562, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
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: 37.87 %
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: 298 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→35.29 Å / Num. obs: 31333 / % possible obs: 98.37 % / Redundancy: 6.94 % / Biso Wilson estimate: 33.53 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.18 / Net I/σ(I): 6.55
Reflection shellResolution: 1.79→1.85 Å / Mean I/σ(I) obs: 0.32 / Num. unique obs: 2855 / CC1/2: 0.14 / Rrim(I) all: 4.04 / % possible all: 89.92

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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→35.29 Å / SU ML: 0.3264 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 27.4702
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2035 1567 4.99 %
Rwork0.1839 29826 -
obs0.1849 31324 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.26 Å2
Refinement stepCycle: LAST / Resolution: 1.79→35.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 0 126 2502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00272506
X-RAY DIFFRACTIONf_angle_d0.62293435
X-RAY DIFFRACTIONf_chiral_restr0.0468409
X-RAY DIFFRACTIONf_plane_restr0.0035438
X-RAY DIFFRACTIONf_dihedral_angle_d5.9141357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.850.42881260.44782442X-RAY DIFFRACTION88.34
1.85-1.910.42441420.40542701X-RAY DIFFRACTION98.51
1.91-1.990.39061440.33462727X-RAY DIFFRACTION98.83
1.99-2.080.31051420.26142703X-RAY DIFFRACTION98.82
2.08-2.190.27751430.2172720X-RAY DIFFRACTION99.1
2.19-2.330.25341440.21342730X-RAY DIFFRACTION99.31
2.33-2.510.22741430.19882723X-RAY DIFFRACTION99.48
2.51-2.760.21161450.18272751X-RAY DIFFRACTION99.66
2.76-3.160.22521440.17522744X-RAY DIFFRACTION99.76
3.16-3.980.18351460.14682766X-RAY DIFFRACTION99.83
3.98-35.290.12641480.14182819X-RAY DIFFRACTION99.7

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