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- PDB-7nkw: Endothiapepsin structure obtained at 298K after a soaking with fr... -

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Basic information

Entry
Database: PDB / ID: 7nkw
TitleEndothiapepsin structure obtained at 298K after a soaking with fragment JFD03909 from a dataset collected with JUNGFRAU detector
ComponentsEndothiapepsin
KeywordsHYDROLASE / FBDD / room temperature / JUNGFRAU
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. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.27 Å
AuthorsEngilberge, S. / Huang, C.-Y. / Leonarski, F. / Wojdyla, J.A. / Marsh, M. / Olieric, V. / Wang, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation200021_182369 Switzerland
CitationJournal: To Be Published
Title: Endothiapepsin structure obtained at 298K after a soaking with fragment JFD03909 from a dataset collected with JUNGFRAU detector
Authors: Engilberge, S. / Huang, C.-Y. / Smith, K.M.L. / Eris, D. / Wojdyla, J.A. / Olieric, V. / Leonarski, F. / Sharpe, M. / Wang, M.
History
DepositionFeb 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)33,8922
Polymers33,8141
Non-polymers781
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint3 kcal/mol
Surface area13240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.005, 74.636, 52.826
Angle α, β, γ (deg.)90.000, 108.390, 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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.55 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 100 mM ammonium acetate, 100 mM sodium acetate pH 4.6 and 26 to 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→43.66 Å / Num. obs: 15626 / % possible obs: 99.31 % / Redundancy: 5.8 % / Biso Wilson estimate: 44.94 Å2 / CC1/2: 0.96 / Rpim(I) all: 0.23 / Net I/σ(I): 3.45
Reflection shellResolution: 2.27→2.35 Å / Mean I/σ(I) obs: 0.58 / Num. unique obs: 1487 / CC1/2: 0.09 / Rpim(I) all: 1.79

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUSTER2.10.3refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RSV

6rsv


Resolution: 2.27→43.66 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.934 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.266 / SU Rfree Blow DPI: 0.2
RfactorNum. reflection% reflectionSelection details
Rfree0.227 781 5 %RANDOM
Rwork0.184 ---
obs0.186 15612 99.3 %-
Displacement parametersBiso max: 122.53 Å2 / Biso mean: 54.94 Å2 / Biso min: 22.32 Å2
Baniso -1Baniso -2Baniso -3
1--11.8022 Å20 Å2-0.3332 Å2
2---2.7896 Å20 Å2
3---14.5918 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: final / Resolution: 2.27→43.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2348 0 4 85 2437
Biso mean--33.29 49.07 -
Num. residues----326
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d958SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes758HARMONIC5
X-RAY DIFFRACTIONt_it4692HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion361SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4542SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4692HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8422HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion13.31
LS refinement shellResolution: 2.27→2.29 Å / Rfactor Rfree error: 0 / Total num. of bins used: 39
RfactorNum. reflection% reflection
Rfree0.269 20 4.99 %
Rwork0.246 381 -
all0.2471 401 -
obs--84.57 %
Refinement TLS params.Method: refined / Origin x: 4.3637 Å / Origin y: 0.6876 Å / Origin z: 5.6119 Å
111213212223313233
T-0.0416 Å20.001 Å2-0.1289 Å2--0.1524 Å2-0.0182 Å2--0.3152 Å2
L0.1229 °2-0.1191 °20.3358 °2-0.1566 °2-0.1231 °2--0.5504 °2
S-0.0088 Å °-0.0329 Å °0.0344 Å °0.0635 Å °-0.0034 Å °-0.0393 Å °-0.0224 Å °-0.0317 Å °0.0122 Å °
Refinement TLS groupSelection details: { A|* }

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