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

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Basic information

Entry
Database: PDB / ID: 5rcw
TitlePanDDA analysis group deposition -- Endothiapepsin ground state model 18
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: 1.04 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

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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)44,14710
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)45.249, 73.017, 52.530
Angle α, β, γ (deg.)90.000, 109.190, 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 / Glycerol


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


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


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


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


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O

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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: 35.05 %
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→42.77 Å / Num. obs: 145990 / % possible obs: 99.1 % / Redundancy: 6.818 % / Biso Wilson estimate: 15.556 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.062 / Χ2: 1.128 / Net I/σ(I): 14.15 / Num. measured all: 1048720
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
1.04-1.16.411.3981.1916065725051243690.5461.5172290.973
1.1-1.186.660.6952.6215664923522232320.8550.753100.988
1.18-1.276.80.4254.414895921906217740.9380.46250.994
1.27-1.396.860.257.2213833020175200860.9770.271100.996
1.39-1.566.80.13412.8212439918291182110.9920.14500.996
1.56-1.86.820.07521.9310992816129160890.9970.08140.998
1.8-2.27.030.04535.989611813672136550.9980.04900.999
2.2-3.116.960.03744.647362410582105620.9990.0400.998
3.11-506.750.03750.6240056593258560.9980.04370.987

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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→42.77 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.415 / SU ML: 0.02 / 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
Rfree0.15328 7843 5.1 %RANDOM
Rwork0.1529 ---
obs0.1533 145990 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.23 Å2 / Biso mean: 13.151 Å2 / Biso min: 8.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å2-0.31 Å2
2--0.03 Å20 Å2
3---0.46 Å2
Refinement stepCycle: final / Resolution: 1.04→42.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 63 341 2773
Biso mean--38.36 28.59 -
Num. residues----330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0132590
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172260
X-RAY DIFFRACTIONr_angle_refined_deg1.9541.6363557
X-RAY DIFFRACTIONr_angle_other_deg1.6091.5595277
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8465365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.31424.88184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.66715339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.301151
X-RAY DIFFRACTIONr_chiral_restr0.1060.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022986
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02529
X-RAY DIFFRACTIONr_mcbond_it1.1381.2011381
X-RAY DIFFRACTIONr_mcbond_other1.1331.1981378
X-RAY DIFFRACTIONr_mcangle_it1.6171.8111738
LS refinement shellResolution: 1.038→1.065 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.15328 7843 -
Rwork0.1529 10388 -
all-18231 -
obs--95.5 %

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