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- PDB-6rsv: Endothiapepsin in complex with 017 -

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Basic information

Entry
Database: PDB / ID: 6rsv
TitleEndothiapepsin in complex with 017
ComponentsEndothiapepsin
KeywordsHYDROLASE / Aspartic Proteinase / Endothiapepsin / Complex with tetrazole / Inhibitor
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
Chem-KHW / 1~{H}-1,2,3,4-tetrazol-5-ylmethyldiazane / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsMagari, F. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Endothiapepsin in complex with 017
Authors: Magari, F. / Heine, A. / Konstantinidou, M. / Sutanto, F. / Haupenthal, J. / Jumde, R.V. / Unver, M.Y. / Camacho, C.J. / Hirsch, A.K.H. / Doemling, A. / Klebe, G.
History
DepositionMay 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release

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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)34,3455
Polymers33,8141
Non-polymers5314
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint1 kcal/mol
Surface area12800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.400, 73.269, 52.947
Angle α, β, γ (deg.)90.00, 109.75, 90.00
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: 33813.855 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 , 5 types, 316 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-KHW / [(1~{R})-1-[1-(phenylmethyl)-1,2,3,4-tetrazol-5-yl]butyl]diazane


Mass: 246.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18N6
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-KHZ / 1~{H}-1,2,3,4-tetrazol-5-ylmethyldiazane


Mass: 114.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6N6
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.45 Å3/Da / Density % sol: 49.86 %
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; crystals obtained by streak-seeding

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.1→42.729 Å / Num. obs: 129009 / % possible obs: 97.7 % / Redundancy: 3.4 % / CC1/2: 1 / Rsym value: 0.029 / Net I/σ(I): 21.25
Reflection shellResolution: 1.1→1.17 Å / Mean I/σ(I) obs: 3.15 / Num. unique obs: 20112 / CC1/2: 0.89 / Rsym value: 0.34 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
MxCuBEdata collection
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.1→42.729 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 11.78
RfactorNum. reflection% reflection
Rfree0.1438 6451 5 %
Rwork0.1263 --
obs0.1271 128984 97.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.1→42.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2367 0 36 312 2715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012558
X-RAY DIFFRACTIONf_angle_d1.1543518
X-RAY DIFFRACTIONf_dihedral_angle_d3.8541160
X-RAY DIFFRACTIONf_chiral_restr0.089414
X-RAY DIFFRACTIONf_plane_restr0.009470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0998-1.11230.22481850.20323511X-RAY DIFFRACTION84
1.1123-1.12540.20632040.17783867X-RAY DIFFRACTION93
1.1254-1.13910.1512160.15014102X-RAY DIFFRACTION98
1.1391-1.15360.15362140.14084073X-RAY DIFFRACTION99
1.1536-1.16870.15862180.13564140X-RAY DIFFRACTION99
1.1687-1.18480.1822150.13444081X-RAY DIFFRACTION98
1.1848-1.20170.14132170.1214120X-RAY DIFFRACTION99
1.2017-1.21960.14932170.12474117X-RAY DIFFRACTION99
1.2196-1.23870.15952160.1374109X-RAY DIFFRACTION98
1.2387-1.2590.16182130.13184048X-RAY DIFFRACTION97
1.259-1.28070.15682130.13744042X-RAY DIFFRACTION98
1.2807-1.3040.15722180.12184135X-RAY DIFFRACTION99
1.304-1.32910.14112190.11014160X-RAY DIFFRACTION99
1.3291-1.35620.13912180.10534156X-RAY DIFFRACTION99
1.3562-1.38570.13052150.11244079X-RAY DIFFRACTION98
1.3857-1.41790.11892160.09894097X-RAY DIFFRACTION98
1.4179-1.45340.13682150.10424080X-RAY DIFFRACTION98
1.4534-1.49270.11952170.09934131X-RAY DIFFRACTION99
1.4927-1.53660.11872160.10024101X-RAY DIFFRACTION99
1.5366-1.58620.10252180.09474149X-RAY DIFFRACTION99
1.5862-1.64290.12272190.09694164X-RAY DIFFRACTION99
1.6429-1.70870.11962170.10264124X-RAY DIFFRACTION99
1.7087-1.78640.11992150.10554084X-RAY DIFFRACTION97
1.7864-1.88060.12282160.1114097X-RAY DIFFRACTION98
1.8806-1.99850.13042150.10824076X-RAY DIFFRACTION98
1.9985-2.15280.11672170.11174134X-RAY DIFFRACTION98
2.1528-2.36940.15372150.12084091X-RAY DIFFRACTION98
2.3694-2.71220.14942160.13584089X-RAY DIFFRACTION97
2.7122-3.41690.1552180.14274155X-RAY DIFFRACTION99
3.4169-42.76170.16692230.15434221X-RAY DIFFRACTION98

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