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- PDB-5r1u: PanDDA analysis group deposition -- Endothiapepsin in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5r1u
TitlePanDDA analysis group deposition -- Endothiapepsin in complex with fragment F2X-Entry B03, 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
2-[(1R)-1-aminopropyl]phenol / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.039 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

Downloads & links

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Assembly

Deposited unit
A: Endothiapepsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5813
Polymers43,2791
Non-polymers3022
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.285, 73.030, 52.702
Angle α, β, γ (deg.)90.000, 109.370, 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: Chemical ChemComp-T9G / 2-[(1R)-1-aminopropyl]phenol


Mass: 151.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13NO / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 35.25 %
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→42.721 Å / Num. obs: 154897 / % possible obs: 99.7 % / Redundancy: 6.822 % / Biso Wilson estimate: 15.767 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.057 / Χ2: 1.219 / Net I/σ(I): 13.74 / Num. measured all: 1056788
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
1.04-1.16.51.4081.0316328225103248170.5971.532120.989
1.1-1.186.760.742.1315909723545235250.8370.80300.999
1.18-1.276.860.4793.4415028621907218970.9190.51931
1.27-1.396.910.2945.6113942320185201690.9670.31810.999
1.39-1.566.860.15810.4512546818295182760.9890.17120.999
1.56-1.86.830.08619.4611023616150161280.9960.094220.999
1.8-2.26.990.04636.499577813693136630.9990.0500.998
2.2-3.116.850.03548.667257410591105660.9990.03800.998
3.11-506.850.02959.0240644593658930.9990.03150.993

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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: 1.039→42.721 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1392 2106 1.36 %
Rwork0.1266 152799 -
obs0.1273 154898 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 51.43 Å2 / Biso mean: 17.8113 Å2 / Biso min: 10.11 Å2
Refinement stepCycle: final / Resolution: 1.039→42.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 50 328 2747
Biso mean--30 31.07 -
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 (%)
1.0388-1.0630.29931360.322698991003597
1.063-1.08950.25621400.26651018210322100
1.0895-1.1190.24941400.22411017810318100
1.119-1.15190.20771400.19081017410314100
1.1519-1.18910.17971400.17171020410344100
1.1891-1.23160.1651400.15511018310323100
1.2316-1.28090.18031400.13781016210302100
1.2809-1.33920.15421400.12091020510345100
1.3392-1.40980.11121400.10781020410344100
1.4098-1.49820.12381400.09791019910339100
1.4982-1.61390.10071400.09261018310323100
1.6139-1.77630.10841400.09851022010360100
1.7763-2.03330.111410.10071022610367100
2.0333-2.56170.1081400.11381023910379100
2.5617-42.75680.14591420.13531034110483100

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