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- PDB-5r35: PanDDA analysis group deposition -- Auto-refined data of Endothia... -

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Basic information

Entry
Database: PDB / ID: 5r35
TitlePanDDA analysis group deposition -- Auto-refined data of Endothiapepsin for ground state model 29, DMSO-Free
ComponentsEndothiapepsin
KeywordsHYDROLASE
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
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.91 Å
AuthorsWollenhaupt, J. / Metz, A. / Barthel, T. / Lima, G.M.A. / Heine, A. / Mueller, U. / Klebe, G. / Weiss, M.S.
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
DepositionFeb 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 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


Theoretical massNumber of molelcules
Total (without water)43,2791
Polymers43,2791
Non-polymers00
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.316, 72.861, 52.687
Angle α, β, γ (deg.)90.000, 109.440, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endothiapepsin / Aspartate protease


Mass: 43278.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell
Source: (natural) Cryphonectria parasitica (chestnut blight fungus)
References: UniProt: P11838, endothiapepsin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 1.9 Å3/Da / Density % sol: 35.1 %
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% PEG4000

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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: 0.91→42.732 Å / Num. obs: 190722 / % possible obs: 82.7 % / Net I/σ(I): 11.86
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
0.91-0.961.861.8280.596927437239142850.2432.0513140.384
0.96-1.033.870.9851.4313517534959230140.5981.0824550.658
1.03-1.116.540.4933.3421329632592307750.9120.533510.944
1.11-1.226.80.2636.4920369029954287140.9720.28360.959
1.22-1.366.920.1779.5818779027144262800.9860.19320.968
1.36-1.576.870.10515.616469723959234080.9940.11400.977
1.57-1.936.950.06624.1614085020260199680.9970.071110.986
1.93-2.727.050.05132.8711106715754156370.9970.05500.993
2.72-506.940.05236.6760727874486640.9960.056280.991

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
REFMAC5.8.0238phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 0.91→42.732 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1268 2097 1.1 %
Rwork0.1188 188622 -
obs0.1195 190722 82.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.66 Å2 / Biso mean: 15.0053 Å2 / Biso min: 8.2 Å2
Refinement stepCycle: final / Resolution: 0.91→42.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 0 368 2737
Biso mean---29.91 -
Num. residues----330
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.9095-0.93070.3335540.36824793484732
0.9307-0.9540.3197690.31626214628341
0.954-0.97980.2712860.28347769785551
0.9798-1.00860.26371100.24819808991865
1.0086-1.04120.25741370.207122961243381
1.0412-1.07840.18241590.1633143681452795
1.0784-1.12160.12651610.1248144561461795
1.1216-1.17260.12511620.101145171467996
1.1726-1.23440.11811630.0969146021476596
1.2344-1.31180.11631630.0969146821484597
1.3118-1.41310.11171650.0946148121497797
1.4131-1.55530.10021660.0922148851505198
1.5553-1.78030.09791670.0995149921515998
1.7803-2.2430.11141680.1062151271529599
2.243-42.7790.13131700.1309153011547199

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