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- PDB-5r22: PanDDA analysis group deposition -- Endothiapepsin in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5r22
TitlePanDDA analysis group deposition -- Endothiapepsin in complex with fragment F2X-Entry E11, DMSO-free
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
[2-(morpholin-4-yl)-1,3-thiazol-5-yl]methanol / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.098 Å
AuthorsWollenhaupt, J. / Metz, A. / Barthel, T. / Lima, G.M.A. / Heine, A. / Mueller, U. / Klebe, G. / Weiss, M.S.
CitationJournal: Structure / Year: 2020
Title: F2X-Universal and F2X-Entry: Structurally Diverse Compound Libraries for Crystallographic Fragment Screening.
Authors: Wollenhaupt, J. / Metz, A. / Barthel, T. / Lima, G.M.A. / Heine, A. / Mueller, U. / Klebe, G. / Weiss, M.S.
History
DepositionFeb 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)43,4792
Polymers43,2791
Non-polymers2001
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.335, 72.989, 52.762
Angle α, β, γ (deg.)90.000, 109.230, 90.000
Int Tables number4
Space group name H-MP1211

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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 / Details: cell
Source: (natural) Cryphonectria parasitica (chestnut blight fungus)
References: UniProt: P11838, endothiapepsin
#2: Chemical ChemComp-RA7 / [2-(morpholin-4-yl)-1,3-thiazol-5-yl]methanol


Mass: 200.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N2O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
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: 35.42 %
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% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.827 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.827 Å / Relative weight: 1
ReflectionResolution: 1.1→42.805 Å / Num. obs: 131339 / % possible obs: 99.1 % / Redundancy: 6.793 % / Biso Wilson estimate: 18.849 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.092 / Χ2: 1.123 / Net I/σ(I): 9.02 / Num. measured all: 895581
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obsCC1/2Rrim(I) allRejects% possible all
1.1-1.166.292.3570.5813495021452204240.3972.5551320.952
1.16-1.246.771.3721.1313640920148201270.6441.48610.999
1.24-1.346.790.7832.1212781018817187980.8440.848230.999
1.34-1.476.670.3734.4411523617285172540.9520.40510.998
1.47-1.646.640.1938.4810399515658156350.9820.209150.999
1.64-1.96.880.11114.859503513817137920.9930.1230.998
1.9-2.327.080.07223.568277011696116740.9960.07800.998
2.32-3.287.020.06228.5163889909890840.9970.06700.998
3.28-5070.05733.1135487506850440.9960.06120.995

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
REFMAC5.8.0238phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.098→42.805 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1701 2088 1.59 %
Rwork0.1561 129245 -
obs0.1566 131338 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 47.53 Å2 / Biso mean: 20.3838 Å2 / Biso min: 12.72 Å2
Refinement stepCycle: final / Resolution: 1.098→42.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 13 270 2652
Biso mean--20 29.58 -
Num. residues----330
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.0977-1.12330.38751320.38358160829295
1.1233-1.15140.40161400.348785998739100
1.1514-1.18250.31231390.343986098748100
1.1825-1.21730.27861400.314386518791100
1.2173-1.25660.29921400.287386248764100
1.2566-1.30150.2461400.247686328772100
1.3015-1.35360.23521390.218186198758100
1.3536-1.41520.22921390.211885958734100
1.4152-1.48980.20281400.191286418781100
1.4898-1.58320.17561400.14286448784100
1.5832-1.70540.1691400.121186508790100
1.7054-1.87710.1371400.114386788818100
1.8771-2.14870.13491410.114686668807100
2.1487-2.7070.12691400.133787018841100
2.707-42.8380.16091430.150887768919100

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