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- PDB-4y3y: Endothiapepsin in complex with fragment B42 -

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Basic information

Entry
Database: PDB / ID: 4y3y
TitleEndothiapepsin in complex with fragment B42
ComponentsEndothiapepsin
KeywordsHYDROLASE / fragment screening / aspartic protease inhibition
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. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Aspergillopepsin-like catalytic domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / 2-AMINO-4-METHYL-PENTAN-1-OL / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.346 Å
AuthorsHuschmann, F.U. / Linnik, J. / Weiss, M.S. / Mueller, U.
Funding support Germany, 1items
OrganizationGrant numberCountry
BMBF05K13RM1 Germany
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Structures of endothiapepsin-fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library.
Authors: Huschmann, F.U. / Linnik, J. / Sparta, K. / Uhlein, M. / Wang, X. / Metz, A. / Schiebel, J. / Heine, A. / Klebe, G. / Weiss, M.S. / Mueller, U.
History
DepositionFeb 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2May 11, 2016Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Jan 10, 2024Group: Refinement description / Category: 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)34,82213
Polymers33,8141
Non-polymers1,00812
Water5,531307
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint3 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.322, 72.909, 52.652
Angle α, β, γ (deg.)90.00, 109.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 319 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-DCL / 2-AMINO-4-METHYL-PENTAN-1-OL / LEUCINOL


Type: peptide-like / Mass: 117.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15NO
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.19 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.1 M ammonium acetate, 0.1 M sodium acetate, 24-30% PEG 4000, crystals obtained by streak seeding

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.346→42.793 Å / Num. obs: 70867 / % possible obs: 99 % / Redundancy: 3.7 % / Rsym value: 0.055 / Net I/σ(I): 18.66
Reflection shellResolution: 1.35→1.43 Å / Redundancy: 3.46 % / Rmerge(I) obs: 0.55 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Cootcoot 0.6.2model building
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3PCW

3pcw


Resolution: 1.346→34.728 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1416 3543 5 %Random selection
Rwork0.1168 ---
obs0.118 70864 99.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.346→34.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2375 0 62 307 2744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092595
X-RAY DIFFRACTIONf_angle_d1.3073568
X-RAY DIFFRACTIONf_dihedral_angle_d11.208867
X-RAY DIFFRACTIONf_chiral_restr0.074422
X-RAY DIFFRACTIONf_plane_restr0.007457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3461-1.36450.2721170.23352226X-RAY DIFFRACTION81
1.3645-1.3840.24541440.20572723X-RAY DIFFRACTION100
1.384-1.40470.19351410.192693X-RAY DIFFRACTION100
1.4047-1.42660.21621430.16742715X-RAY DIFFRACTION100
1.4266-1.450.21451410.16132679X-RAY DIFFRACTION100
1.45-1.4750.19071420.14542686X-RAY DIFFRACTION100
1.475-1.50180.17491430.14842717X-RAY DIFFRACTION100
1.5018-1.53070.15481410.12932679X-RAY DIFFRACTION100
1.5307-1.56190.16791430.11962721X-RAY DIFFRACTION100
1.5619-1.59590.13571430.11422709X-RAY DIFFRACTION100
1.5959-1.6330.16221410.10872687X-RAY DIFFRACTION100
1.633-1.67390.11341420.10622708X-RAY DIFFRACTION100
1.6739-1.71910.16531430.1032705X-RAY DIFFRACTION100
1.7191-1.76970.15441420.09592708X-RAY DIFFRACTION100
1.7697-1.82680.14061440.09082733X-RAY DIFFRACTION100
1.8268-1.89210.11951420.08992702X-RAY DIFFRACTION100
1.8921-1.96790.12331440.08212737X-RAY DIFFRACTION100
1.9679-2.05740.10261430.08042703X-RAY DIFFRACTION100
2.0574-2.16590.09561420.08242704X-RAY DIFFRACTION100
2.1659-2.30160.11941420.08842703X-RAY DIFFRACTION99
2.3016-2.47920.11861430.09972707X-RAY DIFFRACTION100
2.4792-2.72860.12881430.10432725X-RAY DIFFRACTION100
2.7286-3.12320.12731440.112727X-RAY DIFFRACTION100
3.1232-3.93410.13941440.12292731X-RAY DIFFRACTION100
3.9341-34.73950.15891460.15922793X-RAY DIFFRACTION100

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