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- PDB-4y4g: Endothiapepsin in complex with fragment B53 -

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Basic information

Entry
Database: PDB / ID: 4y4g
TitleEndothiapepsin in complex with fragment B53
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 / L-CANAVANINE / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.439 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 1.3Apr 22, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / 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 / _chem_comp.type / _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)34,80312
Polymers33,8141
Non-polymers98911
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint3 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.212, 73.111, 52.579
Angle α, β, γ (deg.)90.00, 109.25, 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, 323 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.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-GGB / L-CANAVANINE / L-2-AMINO-4-(GUANIDINOOXY)BUTYRIC ACID


Type: L-peptide linking / Mass: 176.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12N4O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 35.11 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M ammonium acetate, 0.1 M sodium acetate, 24-30% PEG 400, 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: 1.439→42.685 Å / Num. obs: 57252 / % possible obs: 97.8 % / Redundancy: 3.87 % / Rsym value: 0.073 / Net I/σ(I): 12.19
Reflection shellResolution: 1.44→1.53 Å / Redundancy: 3.94 % / Rmerge(I) obs: 0.606 / % possible all: 95.9

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Processing

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

3pcw


Resolution: 1.439→42.685 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1591 2862 5 %Random selection
Rwork0.1201 ---
obs0.122 57249 97.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.439→42.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2375 0 62 312 2749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082586
X-RAY DIFFRACTIONf_angle_d1.2833555
X-RAY DIFFRACTIONf_dihedral_angle_d11.062865
X-RAY DIFFRACTIONf_chiral_restr0.07420
X-RAY DIFFRACTIONf_plane_restr0.007458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4393-1.46410.25521390.19722634X-RAY DIFFRACTION95
1.4641-1.49080.24311400.18682662X-RAY DIFFRACTION96
1.4908-1.51940.21871390.17242651X-RAY DIFFRACTION96
1.5194-1.55050.22181440.16642723X-RAY DIFFRACTION97
1.5505-1.58420.20321400.15482659X-RAY DIFFRACTION97
1.5842-1.6210.19751410.14362681X-RAY DIFFRACTION97
1.621-1.66160.20741420.13612696X-RAY DIFFRACTION97
1.6616-1.70650.16781410.12912686X-RAY DIFFRACTION98
1.7065-1.75670.17751440.11732729X-RAY DIFFRACTION98
1.7567-1.81340.14721430.10672728X-RAY DIFFRACTION98
1.8134-1.87820.15131430.10012713X-RAY DIFFRACTION98
1.8782-1.95340.12821430.08852716X-RAY DIFFRACTION98
1.9534-2.04230.14721440.08892745X-RAY DIFFRACTION98
2.0423-2.150.14131440.08862722X-RAY DIFFRACTION98
2.15-2.28470.14751440.09352748X-RAY DIFFRACTION99
2.2847-2.46110.14691440.09982737X-RAY DIFFRACTION99
2.4611-2.70870.12111460.10172760X-RAY DIFFRACTION99
2.7087-3.10060.12651460.10732782X-RAY DIFFRACTION99
3.1006-3.9060.14911460.1192770X-RAY DIFFRACTION99
3.906-42.70340.17821490.15552845X-RAY DIFFRACTION100

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