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- PDB-7bkr: Endothiapepsin structure obtained at 298K and 40 mM DMSO from a d... -

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Basic information

Entry
Database: PDB / ID: 7bkr
TitleEndothiapepsin structure obtained at 298K and 40 mM DMSO from a dataset collected with JUNGFRAU detector
ComponentsEndothiapepsin
KeywordsHYDROLASE / FBDD / DMSO
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: 2.1 Å
AuthorsEngilberge, S. / Huang, C.-Y. / Leonarski, F. / Wojdyla, J.A. / Marsh, M. / Olieric, V. / Wang, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation200021_182369 Switzerland
CitationJournal: To Be Published
Title: Endothiapepsin structure obtained at 298K and 40 mM DMSO from a dataset collected with JUNGFRAU detector
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

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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)34,78311
Polymers33,8141
Non-polymers96910
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint17 kcal/mol
Surface area13150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.893, 74.003, 45.817
Angle α, β, γ (deg.)90.000, 108.970, 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-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


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


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.51 Å3/Da / Density % sol: 50.95 %
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: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→43.33 Å / Num. obs: 19537 / % possible obs: 99.6 % / Redundancy: 5.6 % / CC1/2: 0.97 / Rpim(I) all: 0.2427 / Net I/σ(I): 6.65
Reflection shellResolution: 2.1→2.17 Å / Mean I/σ(I) obs: 1.56 / Num. unique obs: 1969 / CC1/2: 0.63 / Rpim(I) all: 0.8456

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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: 2.1→43.33 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.195 977 5 %
Rwork0.147 18560 -
obs0.1494 19537 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.65 Å2 / Biso mean: 39.3817 Å2 / Biso min: 18.32 Å2
Refinement stepCycle: final / Resolution: 2.1→43.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2370 0 55 153 2578
Biso mean--88.79 48.13 -
Num. residues----330
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.210.29391380.20682609274798
2.21-2.350.26421390.176226392778100
2.35-2.530.21471400.162526652805100
2.53-2.780.21251380.14222620275899
2.78-3.180.18851390.134126622801100
3.19-4.010.15241400.128926612801100
4.01-43.330.18711430.14492704284799
Refinement TLS params.Method: refined / Origin x: 3.7454 Å / Origin y: -0.8974 Å / Origin z: 5.6741 Å
111213212223313233
T0.2149 Å20.0018 Å20.0064 Å2-0.214 Å20.006 Å2--0.2046 Å2
L0.481 °20.0494 °20.239 °2-0.6485 °20.1847 °2--0.3604 °2
S0.0248 Å °0.0418 Å °0.0118 Å °0.0825 Å °0.0045 Å °-0.0292 Å °0.0482 Å °0.0569 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 330
2X-RAY DIFFRACTION1allA401 - 1301
3X-RAY DIFFRACTION1allS1 - 152

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