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- PDB-7bks: 100K endothiapepsin structure obtained in presence of 40 mM DMSO -

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Basic information

Entry
Database: PDB / ID: 7bks
Title100K endothiapepsin structure obtained in presence of 40 mM DMSO
ComponentsEndothiapepsin
KeywordsHYDROLASE / DMSO / FBDD
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
DI(HYDROXYETHYL)ETHER / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.24 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: 100K endothiapepsin structure obtained in presence of 40 mM DMSO
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 1.2Oct 9, 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)35,60415
Polymers33,8141
Non-polymers1,79014
Water9,116506
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint18 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.245, 73.013, 52.918
Angle α, β, γ (deg.)90.000, 109.910, 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-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.43 Å3/Da / Density % sol: 49.39 %
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: Aug 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.24→49.75 Å / Num. obs: 69576 / % possible obs: 76.13 % / Redundancy: 6.3 % / CC1/2: 0.99 / Rpim(I) all: 0.0195 / Net I/σ(I): 20.35
Reflection shellResolution: 1.24→1.28 Å / Mean I/σ(I) obs: 1.42 / Num. unique obs: 1320 / CC1/2: 0.62 / Rpim(I) all: 0.51 / % possible all: 14.46

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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: 1.24→49.75 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1558 3408 4.9 %
Rwork0.1429 66164 -
obs0.1435 69572 76.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.65 Å2 / Biso mean: 20.6565 Å2 / Biso min: 7.87 Å2
Refinement stepCycle: final / Resolution: 1.24→49.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2375 0 104 521 3000
Biso mean--47.05 33.99 -
Num. residues----330
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.24-1.260.5464130.3283503639
1.26-1.280.2587250.296459562017
1.28-1.30.243410.270685589624
1.3-1.320.2495540.24821141119531
1.32-1.340.2794720.23431408148039
1.34-1.370.1953790.22331698177747
1.37-1.390.19871050.21082018212356
1.39-1.420.221410.19762305244664
1.42-1.450.19251380.17992641277973
1.45-1.480.22131870.17023000318784
1.48-1.520.20031770.16683441361895
1.52-1.560.16161780.15483546372498
1.56-1.610.17311790.153584376399
1.61-1.660.17981770.15073572374999
1.66-1.720.15292000.15313555375599
1.72-1.790.15921830.1463577376099
1.79-1.870.17031850.1473560374598
1.87-1.970.14771600.140536383798100
1.97-2.090.13962010.12893571377299
2.09-2.250.12961910.12433607379899
2.25-2.480.13061860.13113590377699
2.48-2.840.14271690.13593605377498
2.84-3.580.17071670.135436533820100
3.58-49.750.14432000.1383654385499

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