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- PDB-5r27: PanDDA analysis group deposition -- Endothiapepsin in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5r27
TitlePanDDA analysis group deposition -- Endothiapepsin in complex with fragment F2X-Entry G03, 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
3-ethoxybenzene-1-carboximidamide / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.029 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 13, 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)43,6073
Polymers43,2791
Non-polymers3282
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.243, 73.059, 52.631
Angle α, β, γ (deg.)90.000, 109.660, 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-RD4 / 3-ethoxybenzene-1-carboximidamide


Mass: 164.204 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 1.89 Å3/Da / Density % sol: 35.01 %
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: 1.03→42.605 Å / Num. obs: 151701 / % possible obs: 95.3 % / Redundancy: 7.104 % / Biso Wilson estimate: 15.366 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.079 / Χ2: 1.138 / Net I/σ(I): 10.8 / Num. measured all: 1077751
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
1.03-1.096.331.1631.1916224125628233050.6011.2571630.909
1.09-1.176.740.632.4616281924154226570.8510.67810.938
1.17-1.266.820.4143.915368022541213380.9260.446400.947
1.26-1.386.870.2795.9214207720688197670.9630.320.955
1.38-1.546.790.1661012716918728180590.9850.1800.964
1.54-1.786.770.10216.4511224516569160950.9940.11110.971
1.78-2.187.10.06626.169940713996137260.9970.07100.981
2.18-3.086.950.05731.487570910891107540.9970.06240.987
3.08-506.980.05435.2742404607660170.9970.058150.99

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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: 1.029→42.605 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 13.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1416 2093 1.38 %
Rwork0.1235 149604 -
obs0.1254 151703 95.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.37 Å2 / Biso mean: 16.6131 Å2 / Biso min: 9.23 Å2
Refinement stepCycle: final / Resolution: 1.029→42.605 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 24 326 2719
Biso mean--20 30.05 -
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 (%)
1.0289-1.05280.28091280.39157928588
1.0528-1.07910.30641360.24219661979793
1.0791-1.10830.21051370.1969761989893
1.1083-1.14090.17391380.15969809994794
1.1409-1.17780.1531370.13719817995494
1.1778-1.21990.15521390.124598751001495
1.2199-1.26870.13641390.118299111005095
1.2687-1.32640.13721400.113999951013595
1.3264-1.39640.13941410.104699921013396
1.3964-1.48390.12161410.0968101101025196
1.4839-1.59840.11251430.0937101341027797
1.5984-1.75930.11811430.1004101971034097
1.7593-2.01390.11511440.1022102751041998
2.0139-2.53720.12481450.1171103651051099
2.5372-42.64160.16021480.1402105451069399

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