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- PDB-5qb9: Crystal structure of Endothiapepsin-FRG081 complex -

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Basic information

Entry
Database: PDB / ID: 5qb9
TitleCrystal structure of Endothiapepsin-FRG081 complex
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
ACETATE ION / Chem-D6S / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid Body / Resolution: 1.478 Å
AuthorsHuschmann, F.
CitationJournal: To be published
Title: Crystal structure of Endothiapepsin
Authors: Huschmann, F.U. / Weiss, M.S. / Mueller, U. / Haustedt, L.O. / Klebe, G.
History
DepositionAug 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Advisory / Database references / Structure summary
Category: database_2 / pdbx_deposit_group / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_deposit_group.group_description / _pdbx_deposit_group.group_title
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endothiapepsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4146
Polymers33,8141
Non-polymers6005
Water4,648258
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.256, 72.895, 52.649
Angle α, β, γ (deg.)90.000, 109.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-D6S / (1S,2S,3S,4R,5R)-2-amino-4-[benzyl(methyl)amino]-6,8-dioxabicyclo[3.2.1]octan-3-ol


Mass: 264.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 293 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
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.48→42.761 Å / Num. obs: 53378 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.86 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.077 / Χ2: 0.992 / Net I/σ(I): 12.8 / Num. measured all: 196256
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.48-1.570.6111.9130439870884630.7240.71797.2
1.57-1.680.4142.9230525818080980.8480.48299
1.68-1.810.2724.3226805762675620.9230.32199.2
1.81-1.980.157825855698769150.9760.18399
1.98-2.220.08513.8923622638763430.9920.09999.3
2.22-2.560.06118.8520410559655420.9950.07299
2.56-3.130.04227.3917708476047090.9980.04998.9
3.13-4.410.02939.0613445372236770.9980.03498.8
4.41-42.7610.02543.747447209020690.9980.02999

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Processing

Software
NameVersionClassificationNB
PHENIX1.9_1692refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: Rigid Body / Resolution: 1.478→42.761 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1778 999 1.87 %
Rwork0.1381 52374 -
obs0.1388 53373 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.22 Å2 / Biso mean: 18.183 Å2 / Biso min: 9.38 Å2
Refinement stepCycle: final / Resolution: 1.478→42.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2385 0 41 260 2686
Biso mean--34.27 32.33 -
Num. residues----330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052588
X-RAY DIFFRACTIONf_angle_d13566
X-RAY DIFFRACTIONf_chiral_restr0.04426
X-RAY DIFFRACTIONf_plane_restr0.004461
X-RAY DIFFRACTIONf_dihedral_angle_d10.399884
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4785-1.55640.25821390.18927297743697
1.5564-1.6540.23451430.16057473761699
1.654-1.78170.21611430.14297488763199
1.7817-1.9610.16461420.12377491763399
1.961-2.24470.14541430.11127493763699
2.2447-2.8280.16721440.13937533767799
2.828-42.77910.17381450.14087599774499

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