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- PDB-6zz2: Cocktail experiment E: fragments 52, 58, and 63 at 90 mM concentr... -

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Basic information

Entry
Database: PDB / ID: 6zz2
TitleCocktail experiment E: fragments 52, 58, and 63 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-F63 / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14885439131 Å
AuthorsHassaan, E. / Klebe, G. / Heine, A. / Schiebel, J. / Koester, H.
CitationJournal: To Be Published
Title: Cocktail experiment E: fragments 52, 58, and 63 at 90 mM concentration in complex with Endothiapepsin
Authors: Hassaan, E. / Klebe, G. / Heine, A. / Schiebel, J. / Koester, H. / Softley, C. / Sattler, M.
History
DepositionAug 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 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 6, 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)43,8887
Polymers43,2791
Non-polymers6096
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint4 kcal/mol
Surface area12920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.401, 73.178, 52.659
Angle α, β, γ (deg.)90.000, 109.762, 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

#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
#2: Chemical ChemComp-F63 / N-methyl-1-[5-(pyridin-3-yloxy)furan-2-yl]methanamine


Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O
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: 35.34 %
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: 1.148→41.034 Å / Num. obs: 114661 / % possible obs: 99.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 10.2714223387 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.9
Reflection shellResolution: 1.15→1.22 Å / Num. unique obs: 18351 / CC1/2: 0.768

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Processing

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

5dq4


Resolution: 1.14885439131→41.0334966108 Å / SU ML: 0.0983158818139 / Cross valid method: FREE R-VALUE / σ(F): 1.36387254305 / Phase error: 12.8187442903
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.144551258568 5733 5.00026165681 %
Rwork0.126590205409 108921 -
obs0.127491596249 114654 99.628091274 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.9693194313 Å2
Refinement stepCycle: LAST / Resolution: 1.14885439131→41.0334966108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2372 0 37 315 2724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007352245083212536
X-RAY DIFFRACTIONf_angle_d1.019698042433484
X-RAY DIFFRACTIONf_chiral_restr0.082051223726409
X-RAY DIFFRACTIONf_plane_restr0.00760725295564459
X-RAY DIFFRACTIONf_dihedral_angle_d14.5161168647838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1489-1.16190.2169572257381810.2248251884293439X-RAY DIFFRACTION93.7095521615
1.1619-1.17560.2480808778461890.2016660207483596X-RAY DIFFRACTION99.8680738786
1.1756-1.18990.2111198290471910.1945514050323633X-RAY DIFFRACTION99.9216096159
1.1899-1.2050.2203410584611920.1840681318843647X-RAY DIFFRACTION99.9219156689
1.205-1.22080.2136499763671900.1769158470593614X-RAY DIFFRACTION99.7901364113
1.2208-1.23760.2249033581861910.1765948045443619X-RAY DIFFRACTION99.6599529166
1.2376-1.25520.2155533957281910.1645265572463633X-RAY DIFFRACTION99.7131681877
1.2552-1.2740.1655745322231890.1578254493143597X-RAY DIFFRACTION99.7891407486
1.274-1.29390.1795690401951930.1455973795983653X-RAY DIFFRACTION99.8183233844
1.2939-1.31510.1699243752291890.1407419541153603X-RAY DIFFRACTION99.894625922
1.3151-1.33780.1408762026561920.138906157833647X-RAY DIFFRACTION99.9479302265
1.3378-1.36210.1708302944221910.1320519090033624X-RAY DIFFRACTION99.9476028294
1.3621-1.38830.1624529215061920.130594527843653X-RAY DIFFRACTION99.8441963126
1.3883-1.41660.1508931977921920.1100573290653643X-RAY DIFFRACTION99.8958061995
1.4166-1.44750.1175653209941880.1066598219083582X-RAY DIFFRACTION99.6827075621
1.4475-1.48110.1305322420461910.09910086594923621X-RAY DIFFRACTION99.8428496595
1.4811-1.51820.1218638835531920.09861961053813651X-RAY DIFFRACTION99.9219968799
1.5182-1.55920.1252367118931920.09376730430563642X-RAY DIFFRACTION99.9218139171
1.5592-1.60510.1139558120881910.09295946081743638X-RAY DIFFRACTION99.8175182482
1.6051-1.65690.1197939352451910.0951161288963623X-RAY DIFFRACTION99.9737876802
1.6569-1.71610.1299197890661920.09686589249543651X-RAY DIFFRACTION99.896022875
1.7161-1.78480.1231720695521920.09777494304513654X-RAY DIFFRACTION99.9220576773
1.7848-1.86610.1265118943211920.1021103469843631X-RAY DIFFRACTION100
1.8661-1.96450.1156523842251920.1003059654073664X-RAY DIFFRACTION99.9740731138
1.9645-2.08750.1225965592051910.09946461447813630X-RAY DIFFRACTION99.9215481172
2.0875-2.24870.1162135670911930.1041753651273650X-RAY DIFFRACTION99.7663551402
2.2487-2.4750.1216707934661910.112945266353641X-RAY DIFFRACTION99.6359854394
2.475-2.8330.1419274527861930.1233706420923664X-RAY DIFFRACTION99.7156153051
2.833-3.5690.1474302959261930.1346858427833666X-RAY DIFFRACTION99.8447606727
3.569-410.1672767041331960.1658905637553712X-RAY DIFFRACTION99.5161701044

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