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- PDB-5qbq: Crystal structure of Endothiapepsin -

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Basic information

Entry
Database: PDB / ID: 5qbq
TitleCrystal structure of Endothiapepsin
ComponentsEndothiapepsin
KeywordsHYDROLASE
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 / Chem-DC7 / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.697 Å
AuthorsHuschmann, F.
CitationJournal: To be published
Title: Crystal structure of Endothiapepsin
Authors: Huschmann, F.U. / Weiss, M.S. / Mueller, U. / Haustedt, L.O. / Klebe, G.
History
DepositionAug 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Structure summary / Category: database_2 / pdbx_deposit_group
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_deposit_group.group_description / _pdbx_deposit_group.group_title

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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)34,3765
Polymers33,8141
Non-polymers5624
Water4,666259
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.515, 74.314, 53.739
Angle α, β, γ (deg.)90.000, 110.550, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-DC7 / 4-[2-({methyl[(pyridin-3-yl)methyl]amino}methyl)-1,3-thiazol-4-yl]piperidin-4-ol


Mass: 318.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H22N4OS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 293 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: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.7→42.619 Å / Num. obs: 36384 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.17 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.115 / Rrim(I) all: 0.134 / Χ2: 0.98 / Net I/σ(I): 9.35 / Num. measured all: 137161
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.80.7131.722088596857910.5260.82997
1.8-1.920.5232.2719933560254590.8430.61497.4
1.92-2.080.3593.4919571525951680.8930.41898.3
2.08-2.280.2315.5517232482345300.9550.2793.9
2.28-2.540.1627.2416027435543410.9710.1999.7
2.54-2.930.09512.3615206386638550.990.1199.7
2.93-3.590.05420.7212171328232740.9960.06499.8
3.59-5.060.03730.829635256125300.9980.04398.8
5.06-42.6190.02934.855297144814350.9990.03499.1

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Processing

Software
NameVersionClassificationNB
PHENIX1.9_1692refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
RefinementResolution: 1.697→42.618 Å / SU ML: 0.2 / σ(F): 1.33 / Phase error: 24.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2369 1803 5.01 %
Rwork0.1963 34212 -
obs0.1984 36015 97.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.57 Å2 / Biso mean: 20.7789 Å2 / Biso min: 6.86 Å2
Refinement stepCycle: final / Resolution: 1.697→42.618 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 60 264 2713
Biso mean--31.41 27.03 -
Num. residues----330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062585
X-RAY DIFFRACTIONf_angle_d1.053552
X-RAY DIFFRACTIONf_chiral_restr0.042417
X-RAY DIFFRACTIONf_plane_restr0.005474
X-RAY DIFFRACTIONf_dihedral_angle_d10.555892
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6968-1.74260.32581350.26932558269394
1.7426-1.79390.28771390.25822649278899
1.7939-1.85180.29121430.256227072850100
1.8518-1.9180.39431260.32572379250588
1.918-1.99480.32941330.26182517265093
1.9948-2.08560.21291410.199226782819100
2.0856-2.19550.22391410.184126892830100
2.1955-2.33310.35721280.29542427255590
2.3331-2.51320.23961430.196127132856100
2.5132-2.76610.23611420.183227032845100
2.7661-3.16620.24151440.176327222866100
3.1662-3.98860.18181420.17112709285199
3.9886-42.63160.16781460.128427612907100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4627-0.05970.03070.5133-0.11930.0989-0.06030.04450.05270.27390.06960.0344-0.0589-0.0303-0.00140.16270.01610.02560.09290.00580.09530.2001-8.493414.3965
20.11880.0214-0.09510.01320.00740.09650.07310.02840.0298-0.1161-0.05070.0277-0.0431-0.00240.11660.5070.0703-0.02110.1501-0.00230.09162.9603-1.964725.0208
30.3744-0.0827-0.16030.3979-0.13530.2129-0.0995-0.03350.02830.50590.0283-0.1114-0.25320.0108-0.09770.31510.0206-0.06920.1163-0.00040.10655.7808-2.39218.8618
40.06310.1253-0.11260.26-0.25060.186-0.02750.0886-0.03320.0027-0.0123-0.1219-0.01490.0573-0.00060.0820.0038-0.02050.12440.00640.16914.6952-3.9116-0.4456
50.0573-0.11250.02230.3272-0.08440.02390.01140.07330.13950.1333-0.0323-0.2439-0.0663-0.18790.01420.1077-0.008-0.00780.13790.010.169910.210812.15950.0898
60.1027-0.030.01790.10880.04580.0286-0.01010.00710.04940.0011-0.0032-0.01940.0023-0.008300.0957-0.00330.01170.10070.01890.07620.748712.2539-7.5124
70.0095-0.01290.01270.0896-0.03330.0348-0.11920.10070.090.0350.13060.2613-0.0107-0.037-0.01120.0784-0.0250.04450.1619-0.01050.1522-13.69639.5344-8.1826
80.1144-0.13180.01710.5191-0.15570.28820.00960.00290.02450.0358-0.0567-0.0633-0.04480.0213-0.03550.0591-0.01290.01040.09870.00010.09362.98714.9734-4.3951
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:62)A1 - 62
2X-RAY DIFFRACTION2(chain A and resid 63:81)A63 - 81
3X-RAY DIFFRACTION3(chain A and resid 82:151)A82 - 151
4X-RAY DIFFRACTION4(chain A and resid 152:190)A152 - 190
5X-RAY DIFFRACTION5(chain A and resid 191:204)A191 - 204
6X-RAY DIFFRACTION6(chain A and resid 205:242)A205 - 242
7X-RAY DIFFRACTION7(chain A and resid 243:258)A243 - 258
8X-RAY DIFFRACTION8(chain A and resid 259:330)A259 - 330

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