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- PDB-5rdc: PanDDA analysis group deposition -- Endothiapepsin ground state m... -

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Basic information

Entry
Database: PDB / ID: 5rdc
TitlePanDDA analysis group deposition -- Endothiapepsin ground state model 34
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 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.02 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 30, 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)44,14710
Polymers43,2791
Non-polymers8689
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.275, 72.962, 52.461
Angle α, β, γ (deg.)90.000, 109.090, 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, 343 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 34.99 %
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: 1.02→42.82 Å / Num. obs: 154962 / % possible obs: 99.4 % / Redundancy: 6.756 % / Biso Wilson estimate: 14.984 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.067 / Χ2: 1.125 / Net I/σ(I): 13.04 / Num. measured all: 1103450
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
1.02-1.085.992.0480.7215873626502257700.322.2362620.972
1.08-1.156.731.0011.7216757724908248810.7171.084180.999
1.15-1.256.750.613315668823218231930.8720.66480.999
1.25-1.376.880.3735.1814689321336213100.9490.403260.999
1.37-1.536.860.1959.6813248619309192860.9840.21130.999
1.53-1.766.790.10117.8511596217080170590.9950.10960.999
1.76-2.167.110.04834.2810284814466144430.9990.05200.998
2.16-3.057.020.03447.577856711194111790.9990.03600.999
3.05-506.980.0359.4643693626162200.9990.032120.993

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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: 1.02→42.82 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.455 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1621 8365 5.1 %RANDOM
Rwork0.1617 ---
obs0.1621 154962 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.64 Å2 / Biso mean: 12.914 Å2 / Biso min: 7.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å2-0.32 Å2
2--0.03 Å20 Å2
3---0.34 Å2
Refinement stepCycle: final / Resolution: 1.02→42.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 63 341 2773
Biso mean--38.53 29.29 -
Num. residues----330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0132590
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172260
X-RAY DIFFRACTIONr_angle_refined_deg1.9661.6363557
X-RAY DIFFRACTIONr_angle_other_deg1.6121.5595277
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8585365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.01924.88184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.60615339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.535151
X-RAY DIFFRACTIONr_chiral_restr0.1070.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022986
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02529
X-RAY DIFFRACTIONr_mcbond_it1.1551.1691381
X-RAY DIFFRACTIONr_mcbond_other1.1521.1661378
X-RAY DIFFRACTIONr_mcangle_it1.6621.7621738
LS refinement shellResolution: 1.018→1.045 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.1621 8365 -
Rwork0.1617 10747 -
all-19112 -
obs--94 %

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