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- PDB-7adg: Cocktail experiment G: fragments 216 and 338 at 90 mM concentrati... -

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Basic information

Entry
Database: PDB / ID: 7adg
TitleCocktail experiment G: fragments 216 and 338 at 90 mM concentration in complex with Endothiapepsin
ComponentsEndothiapepsin
KeywordsHYDROLASE / aspartic protease / monomer
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-483 / Chem-8NE / ACETATE ION / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07946365588 Å
AuthorsHassaan, E. / Klebe, G. / Heine, A. / Schiebel, J. / Koester, H.
CitationJournal: To Be Published
Title: Comparison of Cocktail Screening in X-Ray Crystallography vs NMR
Authors: Hassaan, E. / Klebe, G. / Heine, A. / Schiebel, J. / Koester, H.
History
DepositionSep 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)44,23110
Polymers43,2791
Non-polymers9529
Water7,008389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint9 kcal/mol
Surface area12920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.358, 73.192, 52.740
Angle α, β, γ (deg.)90.000, 109.731, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Endothiapepsin / Aspartate protease


Mass: 43278.664 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 , 6 types, 398 molecules

#2: Chemical ChemComp-483 / 2-(1H-imidazol-1-yl)-N-(trans-4-methylcyclohexyl)acetamide


Mass: 221.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-8NE / [azanyl-[4-(trifluoromethyl)phenyl]methylidene]azanium


Mass: 189.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8F3N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 1.9 Å3/Da / Density % sol: 35.4 %
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.08→42.7 Å / Num. obs: 138339 / % possible obs: 99.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 8.98695266584 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.6
Reflection shellResolution: 1.08→1.14 Å / Num. unique obs: 22228 / CC1/2: 0.775

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DQ4

5dq4


Resolution: 1.07946365588→26.895082891 Å / SU ML: 0.0724161707854 / Cross valid method: FREE R-VALUE / σ(F): 1.36531898138 / Phase error: 12.6809857329
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.143567303905 6916 4.99971083222 %
Rwork0.125910237443 131412 -
obs0.126786721834 138328 99.7303571686 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.7713797583 Å2
Refinement stepCycle: LAST / Resolution: 1.07946365588→26.895082891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2372 0 52 389 2813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007262994227232605
X-RAY DIFFRACTIONf_angle_d1.022574057623582
X-RAY DIFFRACTIONf_chiral_restr0.08112876987417
X-RAY DIFFRACTIONf_plane_restr0.00733590693221476
X-RAY DIFFRACTIONf_dihedral_angle_d14.6698136674862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0795-1.09170.247482943212200.2366020002684197X-RAY DIFFRACTION96.6097987752
1.0917-1.10460.2334671206712330.208511819694417X-RAY DIFFRACTION99.914052428
1.1046-1.1180.1968752428282290.1894630298554349X-RAY DIFFRACTION99.7820401046
1.118-1.13220.2073526577642300.1754619239974377X-RAY DIFFRACTION99.8482878197
1.1322-1.14710.1985419662072310.1682904028654373X-RAY DIFFRACTION99.8698481562
1.1471-1.16280.171839301212300.1630725095714368X-RAY DIFFRACTION99.7829861111
1.1628-1.17940.1840450445922290.160888715514357X-RAY DIFFRACTION99.6956521739
1.1794-1.1970.1863530055042300.1541098429224368X-RAY DIFFRACTION99.7613365155
1.197-1.21570.1747910886282300.1527158320264373X-RAY DIFFRACTION99.783221331
1.2157-1.23570.1616673638282310.1455960977294383X-RAY DIFFRACTION99.935022742
1.2357-1.2570.1507982675872300.1371278433384386X-RAY DIFFRACTION99.8917983121
1.257-1.27980.1699693727992280.1340912029924323X-RAY DIFFRACTION99.9341238472
1.2798-1.30440.1636770408392330.1324259221244422X-RAY DIFFRACTION99.9785223368
1.3044-1.33110.1466810028742300.1269708001284383X-RAY DIFFRACTION99.9133636561
1.3311-1.360.1458088313082300.1236695093374372X-RAY DIFFRACTION99.8048145738
1.36-1.39160.1439720922812310.1152147645344379X-RAY DIFFRACTION99.8483863981
1.3916-1.42640.1367435493512310.1088807067764389X-RAY DIFFRACTION99.805573558
1.4264-1.4650.1335763205412310.1048878626194384X-RAY DIFFRACTION99.8485504111
1.465-1.50810.1282272347812310.1030853136224387X-RAY DIFFRACTION99.9567099567
1.5081-1.55680.1101906219932300.09996671523074386X-RAY DIFFRACTION99.9350508768
1.5568-1.61240.1272804908152300.09968507470014360X-RAY DIFFRACTION99.7826086957
1.6124-1.6770.1171539725062310.09955783604854390X-RAY DIFFRACTION99.7625215889
1.677-1.75330.1280705876542320.1020618002694406X-RAY DIFFRACTION99.9568965517
1.7533-1.84570.1344180619712310.1036301448964385X-RAY DIFFRACTION99.8701860666
1.8457-1.96130.1088484098392320.09993406137144418X-RAY DIFFRACTION99.8282524689
1.9613-2.11270.1108207443822300.09980775867054376X-RAY DIFFRACTION99.8699045967
2.1127-2.32520.1307780960012320.1031872108974394X-RAY DIFFRACTION99.8058252427
2.3252-2.66140.1237552157762320.1148162603654413X-RAY DIFFRACTION99.806617963
2.6614-3.35210.1350540505982330.1272541802394428X-RAY DIFFRACTION99.8928418345
3.3521-26.890.1640956271092350.153249239954469X-RAY DIFFRACTION99.5134334673

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