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- PDB-5r3p: PanDDA analysis group deposition -- Auto-refined data of Endothia... -

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Basic information

Entry
Database: PDB / ID: 5r3p
TitlePanDDA analysis group deposition -- Auto-refined data of Endothiapepsin for ground state model 49, 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: 1.077 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
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.076, 73.584, 52.444
Angle α, β, γ (deg.)90.000, 109.060, 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.: 264 / 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: 1.08→42.604 Å / Num. obs: 138398 / % possible obs: 99.3 % / Net I/σ(I): 10.36
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
1.08-1.146.432.2640.614436222462216720.412.4541190.965
1.14-1.226.781.2931.1614354421164211510.6661.39900.999
1.22-1.326.880.8641.8813526419664196480.8010.934210.999
1.32-1.446.820.4933.4512362918129181140.920.53440.999
1.44-1.626.80.2467.111143716381163650.9750.266190.999
1.62-1.866.870.12314.229951214489144720.9930.13310.999
1.86-2.286.950.06228.098538912294122690.9980.06810.998
2.28-3.226.880.04438.7365472951694990.9990.04700.998
3.22-506.980.03549.7437113531753020.9990.03820.997

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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: 1.077→42.604 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1663 2103 1.52 %
Rwork0.1539 136301 -
obs0.1541 138398 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.67 Å2 / Biso mean: 19.3905 Å2 / Biso min: 11.64 Å2
Refinement stepCycle: final / Resolution: 1.077→42.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 0 264 2633
Biso mean---29 -
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 (%)
1.0771-1.10220.42331270.41418314844191
1.1022-1.12970.3741410.334991279268100
1.1297-1.16030.2911400.302591019241100
1.1603-1.19440.30581400.278290879227100
1.1944-1.2330.26571410.252991249265100
1.233-1.2770.27551390.227691099248100
1.277-1.32820.24051410.201791619302100
1.3282-1.38860.1961410.180791029243100
1.3886-1.46180.1821400.158591229262100
1.4618-1.55340.18641410.139491389279100
1.5534-1.67340.14961400.12191459285100
1.6734-1.84180.15351410.120291179258100
1.8418-2.10830.13121410.117291999340100
2.1083-2.65620.14771420.129791869328100
2.6562-42.63760.14191420.149992699411100

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