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- PDB-5rbo: PanDDA analysis group deposition -- Endothiapepsin changed state ... -

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Basic information

Entry
Database: PDB / ID: 5rbo
TitlePanDDA analysis group deposition -- Endothiapepsin changed state model for fragment F2X-Entry Library A07a
ComponentsEndothiapepsin
KeywordsHYDROLASE / FragMAX / FragMAXapp / fragment screening / inhibition / F2X-Entry
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 / (2-aminopyridin-3-yl)methanol / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.08 Å
AuthorsWeiss, M.S. / Wollenhaupt, J. / Metz, A. / Barthel, T. / Lima, G.M.A. / Heine, A. / Mueller, U. / Klebe, G.
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
DepositionMar 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 24, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)43,8266
Polymers43,2791
Non-polymers5485
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.215, 73.139, 52.587
Angle α, β, γ (deg.)90.000, 108.980, 90.000
Int Tables number4
Space group name H-MP1211

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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, 208 molecules

#2: Chemical ChemComp-R8A / (2-aminopyridin-3-yl)methanol


Mass: 124.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / 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: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 35.26 %
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% PEG 4000

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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: 1.08→42.79 Å / Num. obs: 128567 / % possible obs: 96.9 % / Redundancy: 6.618 % / Biso Wilson estimate: 16.597 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.111 / Rrim(I) all: 0.12 / Χ2: 0.975 / Net I/σ(I): 8.21 / Num. measured all: 901669
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
1.07-1.146.081.8280.9913784122660207430.3381.983060.915
1.14-1.226.581.3111.5114017121296205510.451.42270.965
1.22-1.326.541.0222.0312950419803192770.7111.109300.973
1.32-1.446.220.6473.5311363818265178730.8950.706110.979
1.44-1.616.270.3567.4610378616565162650.970.38950.982
1.61-1.866.880.19413.2810030814586144410.9870.21130.99
1.86-2.286.710.09820.718314012395123140.9930.10710.993
2.28-3.216.380.06925.6261221959895210.9950.07510.992
3.21-505.980.05928.9332060536152570.9950.064340.981

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
REFMAC5.8.0238phasing
PHENIX1.16.3549refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.08→42.79 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.988 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20078 6932 5.1 %RANDOM
Rwork0.20036 ---
obs0.2008 128567 97.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.09 Å2 / Biso mean: 13.808 Å2 / Biso min: 5.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20.02 Å2
2--0 Å20 Å2
3---0.47 Å2
Refinement stepCycle: final / Resolution: 1.08→42.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 51 213 2633
Biso mean--37.2 26.49 -
Num. residues----330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133739
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173150
X-RAY DIFFRACTIONr_angle_refined_deg1.7741.6325227
X-RAY DIFFRACTIONr_angle_other_deg1.6281.5737402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.2035.104579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.15825.246122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.75115486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.554151
X-RAY DIFFRACTIONr_chiral_restr0.0930.2533
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025091
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02820
X-RAY DIFFRACTIONr_mcbond_it1.1391.3682065
X-RAY DIFFRACTIONr_mcbond_other1.1331.3662065
X-RAY DIFFRACTIONr_mcangle_it1.6772.0552715
LS refinement shellResolution: 1.078→1.106 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.20078 6932 -
Rwork0.20036 8792 -
all-15724 -
obs--91.1 %

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