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- PDB-5rc8: PanDDA analysis group deposition -- Endothiapepsin changed state ... -

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Basic information

Entry
Database: PDB / ID: 5rc8
TitlePanDDA analysis group deposition -- Endothiapepsin changed state model for fragment F2X-Entry Library G02a
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 / methyl [3-(aminomethyl)phenoxy]acetate / 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 1.2Oct 23, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)44,19710
Polymers43,2791
Non-polymers9189
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.195, 72.971, 52.423
Angle α, β, γ (deg.)90.000, 109.100, 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 , 7 types, 228 molecules

#2: Chemical ChemComp-RCV / methyl [3-(aminomethyl)phenoxy]acetate


Mass: 195.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13NO3 / 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.: 4 / 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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 34.83 %
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→42.74 Å / Num. obs: 146447 / % possible obs: 99.5 % / Redundancy: 6.729 % / Biso Wilson estimate: 16.206 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.06 / Χ2: 1.253 / Net I/σ(I): 13.31 / Num. measured all: 1037053
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
1.04-1.16.391.570.9415982725010244640.4471.7082320.978
1.1-1.186.720.8012.1115748923426234080.7570.8700.999
1.18-1.276.830.4843.714954021886218730.9030.52510.999
1.27-1.396.860.2866.2413811520120201010.9630.3130.999
1.39-1.566.760.15411.5712346518265182360.9880.16720.998
1.56-1.86.670.08520.8410728716097160640.9960.092220.998
1.8-2.26.760.04935.229217513636136050.9980.05300.998
2.2-3.116.660.03943.567028810561105300.9990.04200.997
3.11-506.560.03349.3138867592458510.9990.035430.988

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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→42.74 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.954 / SU B: 0.558 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / 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
Rfree0.1589 7684 5 %RANDOM
Rwork0.15792 ---
obs0.1589 146447 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.19 Å2 / Biso mean: 13.369 Å2 / Biso min: 3.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å2-0.14 Å2
2---0.11 Å20 Å2
3---0.33 Å2
Refinement stepCycle: final / Resolution: 1.04→42.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 86 248 2703
Biso mean--32.91 25.26 -
Num. residues----330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0134088
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183392
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.6285762
X-RAY DIFFRACTIONr_angle_other_deg1.6131.5797993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0815635
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.87125.105143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.26115523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.139151
X-RAY DIFFRACTIONr_chiral_restr0.0920.2555
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025328
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02951
X-RAY DIFFRACTIONr_mcbond_it1.0331.3182204
X-RAY DIFFRACTIONr_mcbond_other1.0261.3172200
X-RAY DIFFRACTIONr_mcangle_it1.5541.9822949
LS refinement shellResolution: 1.038→1.065 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.1589 7684 -
Rwork0.15792 10299 -
all-17983 -
obs--95.3 %

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