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- PDB-5r37: PanDDA analysis group deposition -- Auto-refined data of Endothia... -

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Basic information

Entry
Database: PDB / ID: 5r37
TitlePanDDA analysis group deposition -- Auto-refined data of Endothiapepsin for ground state model 31, 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: 1.038 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
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.205, 73.225, 52.455
Angle α, β, γ (deg.)90.000, 109.280, 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 / Water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 35.04 %
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: 1.04→42.67 Å / Num. obs: 148690 / % possible obs: 95.9 % / Net I/σ(I): 10.04
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
1.04-1.16.461.9340.7316176925023231100.4852.088980.924
1.1-1.186.751.0051.5615863723488221910.7631.08380.945
1.18-1.276.840.6692.4514967421872208580.8640.721380.954
1.27-1.396.880.422413863420150193770.940.45450.962
1.39-1.566.830.2267.5512483618268176980.9790.24420.969
1.56-1.86.80.12513.9310955816105157380.9920.135250.977
1.8-2.27.010.06826.129562613648134190.9970.07320.983
2.2-3.116.920.05134.87313010574104730.9980.05510.99
3.11-506.970.04241.8441280592458810.9980.04670.993

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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: 1.038→42.67 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 18.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.155 2096 1.41 %
Rwork0.1337 146590 -
obs0.1363 148690 95.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.65 Å2 / Biso mean: 17.1716 Å2 / Biso min: 9.83 Å2
Refinement stepCycle: final / Resolution: 1.038→42.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 0 308 2677
Biso mean---30.83 -
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 (%)
1.0385-1.06260.42651320.39629162929490
1.0626-1.08920.33961360.31939502963894
1.0892-1.11860.32881370.25899564970194
1.1186-1.15160.22271370.21969558969595
1.1516-1.18870.20851390.19729715985495
1.1887-1.23120.19931380.18099637977595
1.2312-1.28050.19441390.17189679981896
1.2805-1.33880.18981400.15279790993096
1.3388-1.40940.15541410.12719821996296
1.4094-1.49770.13891410.106898671000897
1.4977-1.61330.11981420.101298981004097
1.6133-1.77570.10181420.097999511009398
1.7757-2.03270.12441440.1007100471019198
2.0327-2.56090.12711450.1172101111025699
2.5609-42.70580.17111470.1396102881043599

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