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- PDB-7bku: Endothiapepsin structure obtained at 100K with fragment JFD03909 bound -

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Basic information

Entry
Database: PDB / ID: 7bku
TitleEndothiapepsin structure obtained at 100K with fragment JFD03909 bound
ComponentsEndothiapepsin
KeywordsHYDROLASE / FBDD / inhibitor
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
1,10-PHENANTHROLINE / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsEngilberge, S. / Huang, C.-Y. / Smith, K.M.L. / Eris, D. / Marsh, M. / Wang, M. / Wojdyla, J.A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation200021_182369 Switzerland
CitationJournal: To Be Published
Title: Endothiapepsin structure obtained at 100K with fragment JFD03909 bound
Authors: Engilberge, S. / Huang, C.-Y. / Smith, K.M.L. / Eris, D. / Wojdyla, J.A. / Olieric, V. / Leonarski, F. / Sharpe, M. / Wang, M.
History
DepositionJan 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 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 13, 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

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Assembly

Deposited unit
A: Endothiapepsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,94727
Polymers33,8141
Non-polymers2,13426
Water9,350519
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint50 kcal/mol
Surface area13590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.286, 73.329, 52.756
Angle α, β, γ (deg.)90.000, 109.690, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endothiapepsin / Aspartate protease


Mass: 33813.855 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-PHN / 1,10-PHENANTHROLINE


Mass: 180.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H8N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / 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: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 100 mM ammonium acetate, 100 mM sodium acetate pH 4.6 and 26 to 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→49.67 Å / Num. obs: 59946 / % possible obs: 94.44 % / Redundancy: 6.7 % / CC1/2: 0.99 / Rpim(I) all: 0.04388 / Net I/σ(I): 12.19
Reflection shellResolution: 1.4→1.45 Å / Mean I/σ(I) obs: 1.18 / Num. unique obs: 4212 / CC1/2: 0.45 / Rpim(I) all: 0.7345

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RSV

6rsv


Resolution: 1.4→49.67 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1802 2985 4.99 %
Rwork0.152 56878 -
obs0.1534 59863 94.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.69 Å2 / Biso mean: 18.7475 Å2 / Biso min: 8.72 Å2
Refinement stepCycle: final / Resolution: 1.4→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2384 0 114 527 3025
Biso mean--39.53 30.81 -
Num. residues----330
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.430.3044930.30081771186462
1.43-1.450.32871010.28982024212571
1.45-1.480.34551090.27032285239480
1.48-1.510.28091370.26482665280292
1.51-1.540.25731610.24482732289397
1.54-1.570.22911530.22652818297198
1.57-1.610.26481210.21952811293298
1.61-1.650.23031630.20712791295498
1.65-1.690.24121520.18392850300299
1.69-1.740.2031320.17862828296099
1.74-1.80.17721700.16392791296199
1.8-1.860.18451280.16692778290697
1.86-1.940.17271660.14122837300399
1.94-2.020.17791480.130328502998100
2.02-2.130.17271280.12652878300699
2.13-2.260.14951540.122628863040100
2.26-2.440.16331580.132528312989100
2.44-2.680.17831580.13272801295997
2.68-3.070.16231510.13328633014100
3.07-3.870.17031550.122128813036100
3.87-49.670.14421470.14862907305499

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