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- PDB-7bky: Endothiapepsin structure obtained at 298K with fragment BTB09871 ... -

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Basic information

Entry
Database: PDB / ID: 7bky
TitleEndothiapepsin structure obtained at 298K with fragment BTB09871 bound from a dataset collected with JUNGFRAU detector
ComponentsEndothiapepsin
KeywordsHYDROLASE / FBDD / room temperature / JUNGFRAU
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
Chem-U1E / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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 with fragment BTB09871 bound 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)35,67321
Polymers33,8141
Non-polymers1,85920
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint33 kcal/mol
Surface area13110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.762, 74.007, 53.339
Angle α, β, γ (deg.)90.000, 109.330, 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-U1E / ~{N}1,~{N}1,~{N}8,~{N}8-tetramethylnaphthalene-1,8-diamine


Mass: 214.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


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


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.2 %
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: 1.9→43.18 Å / Num. obs: 26345 / % possible obs: 98.82 % / Redundancy: 6.8 % / CC1/2: 0.989 / Rpim(I) all: 0.1072 / Net I/σ(I): 5.62
Reflection shellResolution: 1.9→1.96 Å / Mean I/σ(I) obs: 0.82 / Num. unique obs: 2556 / CC1/2: 0.353 / Rpim(I) all: 0.6821

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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: 1.9→43.18 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1987 1318 5 %
Rwork0.1666 25027 -
obs0.1682 26345 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.41 Å2 / Biso mean: 29.6402 Å2 / Biso min: 13.57 Å2
Refinement stepCycle: final / Resolution: 1.9→43.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2380 0 96 191 2667
Biso mean--74.6 41.6 -
Num. residues----330
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.970.33861430.31162721286498
1.97-2.060.32181450.25462752289798
2.06-2.170.27291450.21762755290098
2.17-2.310.23851460.20812767291399
2.31-2.480.20761460.18922764291099
2.48-2.730.20181460.17032792293899
2.74-3.130.19051480.14462800294899
3.13-3.940.13251470.120228062953100
3.94-43.180.18021520.142828703022100
Refinement TLS params.Method: refined / Origin x: 3.843 Å / Origin y: 0.6379 Å / Origin z: 5.4864 Å
111213212223313233
T0.151 Å2-0.0051 Å20.0045 Å2-0.1554 Å2-0.0094 Å2--0.164 Å2
L0.3943 °2-0.1452 °20.2481 °2-0.7281 °2-0.2553 °2--0.8087 °2
S-0.0249 Å °-0.0477 Å °0.0184 Å °0.0556 Å °-0.0045 Å °-0.0657 Å °-0.0204 Å °-0.032 Å °0.0266 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 330
2X-RAY DIFFRACTION1allA401 - 701
3X-RAY DIFFRACTION1allS1 - 200
4X-RAY DIFFRACTION1allB1 - 18

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