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

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Basic information

Entry
Database: PDB / ID: 5rcc
TitlePanDDA analysis group deposition -- Endothiapepsin changed state model for fragment F2X-Entry Library H02b
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 / 3-cyclopentyl-1-(piperazin-1-yl)propan-1-one / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.04 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 1.2Nov 6, 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)44,1138
Polymers43,2791
Non-polymers8347
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.172, 72.854, 52.521
Angle α, β, γ (deg.)90.000, 109.210, 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 , 5 types, 212 molecules

#2: Chemical ChemComp-RDV / 3-cyclopentyl-1-(piperazin-1-yl)propan-1-one


Mass: 210.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H22N2O / 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.: 3 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 1.89 Å3/Da / Density % sol: 34.77 %
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: 1.04→42.69 Å / Num. obs: 142033 / % possible obs: 97.4 % / Redundancy: 6.777 % / Biso Wilson estimate: 16.695 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.064 / Χ2: 1.224 / Net I/σ(I): 12.93 / Num. measured all: 1014573
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
1.04-1.15.582.8130.613839524813210500.2523.053510.848
1.1-1.186.741.3911.3315666223251232350.5711.50780.999
1.18-1.276.820.8442.3214809621709216900.7840.914100.999
1.27-1.46.860.4794.1813700919974199540.9170.519100.999
1.4-1.566.80.2318.4712323518118180880.980.2500.998
1.56-1.86.750.1117.0610761815951159290.9940.11920.999
1.8-2.26.870.0534.819294513536134970.9980.05510.997
2.2-3.116.750.03448.597071310480104570.9990.03700.998
3.11-506.790.02660.9339900587258330.9990.028110.993

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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: 1.04→42.69 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.711 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17018 7626 5.1 %RANDOM
Rwork0.16969 ---
obs0.1702 142033 97.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.32 Å2 / Biso mean: 13.664 Å2 / Biso min: 3.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å2-0.29 Å2
2---0.17 Å20 Å2
3---0.44 Å2
Refinement stepCycle: final / Resolution: 1.04→42.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2373 0 92 240 2705
Biso mean--25.51 25.61 -
Num. residues----329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0133996
X-RAY DIFFRACTIONr_bond_other_d0.0020.0183395
X-RAY DIFFRACTIONr_angle_refined_deg1.8641.6445595
X-RAY DIFFRACTIONr_angle_other_deg1.6211.6088017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9685611
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.52425.448134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.27715531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.204151
X-RAY DIFFRACTIONr_chiral_restr0.0880.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025097
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02878
X-RAY DIFFRACTIONr_mcbond_it1.0631.3452169
X-RAY DIFFRACTIONr_mcbond_other1.0611.3442169
X-RAY DIFFRACTIONr_mcangle_it1.612.0252875
LS refinement shellResolution: 1.04→1.067 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.17018 7626 -
Rwork0.16969 7113 -
all-14739 -
obs--66.2 %

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