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- PDB-4y38: Endothiapepsin in complex with fragment B29 -

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Basic information

Entry
Database: PDB / ID: 4y38
TitleEndothiapepsin in complex with fragment B29
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
methyl L-phenylalaninate / ACETATE ION / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2May 11, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endothiapepsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,02115
Polymers33,8141
Non-polymers1,20714
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint5 kcal/mol
Surface area12990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.052, 72.900, 52.099
Angle α, β, γ (deg.)90.00, 108.73, 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.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-0A9 / methyl L-phenylalaninate


Type: L-peptide linking / Mass: 179.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 1.87 Å3/Da / Density % sol: 34.3 %
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 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: Jul 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.1→42.67 Å / Num. obs: 125104 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7766 % / Rsym value: 0.053 / Net I/σ(I): 13.75
Reflection shellResolution: 1.1→1.17 Å / Redundancy: 3.74 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 2.65 / % possible all: 92.4

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Processing

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

3pcw


Resolution: 1.1→42.667 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1297 6255 5 %Random selection
Rwork0.1145 ---
obs0.1153 125102 96.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.1→42.667 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 75 305 2756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072613
X-RAY DIFFRACTIONf_angle_d1.2623593
X-RAY DIFFRACTIONf_dihedral_angle_d10.809882
X-RAY DIFFRACTIONf_chiral_restr0.072423
X-RAY DIFFRACTIONf_plane_restr0.006467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0995-1.1120.21371920.2163631X-RAY DIFFRACTION90
1.112-1.12510.20491980.20143762X-RAY DIFFRACTION92
1.1251-1.13890.21941970.18863760X-RAY DIFFRACTION92
1.1389-1.15330.19662020.17943830X-RAY DIFFRACTION94
1.1533-1.16840.21142020.17023839X-RAY DIFFRACTION95
1.1684-1.18450.1832060.16473918X-RAY DIFFRACTION95
1.1845-1.20140.18512010.15693817X-RAY DIFFRACTION95
1.2014-1.21930.17782070.15083930X-RAY DIFFRACTION96
1.2193-1.23840.17272050.14093902X-RAY DIFFRACTION96
1.2384-1.25870.14592080.13423936X-RAY DIFFRACTION96
1.2587-1.28040.14992070.13533938X-RAY DIFFRACTION97
1.2804-1.30370.16392070.12983943X-RAY DIFFRACTION97
1.3037-1.32870.16582090.12433960X-RAY DIFFRACTION97
1.3287-1.35590.12242090.11993979X-RAY DIFFRACTION97
1.3559-1.38530.12932100.11183980X-RAY DIFFRACTION97
1.3853-1.41760.14152090.10343971X-RAY DIFFRACTION98
1.4176-1.4530.13032110.1024010X-RAY DIFFRACTION98
1.453-1.49230.12892100.09283996X-RAY DIFFRACTION98
1.4923-1.53620.1162090.09293972X-RAY DIFFRACTION98
1.5362-1.58580.10632110.08734003X-RAY DIFFRACTION98
1.5858-1.64250.1062120.08514027X-RAY DIFFRACTION99
1.6425-1.70830.11072120.08674039X-RAY DIFFRACTION99
1.7083-1.7860.10462140.08794053X-RAY DIFFRACTION99
1.786-1.88020.10672130.08434051X-RAY DIFFRACTION99
1.8802-1.9980.10222140.0844075X-RAY DIFFRACTION99
1.998-2.15220.10322150.08274073X-RAY DIFFRACTION99
2.1522-2.36880.0982150.08924101X-RAY DIFFRACTION100
2.3688-2.71150.10222150.09924083X-RAY DIFFRACTION100
2.7115-3.4160.12122170.10864107X-RAY DIFFRACTION100
3.416-42.6990.14632180.15014161X-RAY DIFFRACTION99

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