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- PDB-7h5v: Crystal structure of endothiapepsin PF_cryo1 in complex with JFD0... -

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Basic information

Entry
Database: PDB / ID: 7h5v
TitleCrystal structure of endothiapepsin PF_cryo1 in complex with JFD03909 at 100 K
ComponentsEndothiapepsin
KeywordsHYDROLASE / Endopeptidase / room temperature
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
1,10-PHENANTHROLINE / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.985 Å
AuthorsHuang, C.-Y. / Aumonier, S. / Olieric, V. / Wang, M.
Funding support Switzerland, European Union, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation182369 Switzerland
H2020 Marie Curie Actions of the European Commission884104European Union
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2024
Title: Cryo2RT: a high-throughput method for room-temperature macromolecular crystallography from cryo-cooled crystals.
Authors: Huang, C.Y. / Aumonier, S. / Olieric, V. / Wang, M.
History
DepositionApr 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)37,35445
Polymers33,8141
Non-polymers3,54044
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.234, 73.263, 52.661
Angle α, β, γ (deg.)90.00, 109.53, 90.00
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.: 43 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-PHN / 1,10-PHENANTHROLINE


Mass: 180.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H8N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 49.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M ammonium acetate, 0.1 M sodium acetate pH 4.6, and 26 - 30% (v/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→42.63 Å / Num. obs: 22338 / % possible obs: 99 % / Biso Wilson estimate: 22.09 Å2 / Rmerge F all: 0.1 / CC1/2: 0.99 / Net I/σ(I): 15.75
Reflection shellResolution: 1.99→2.08 Å / Redundancy: 7.15 % / Rmerge F all: 0.33 / Num. unique obs: 3541 / CC1/2: 0.96 / Net I/σ(I) all: 5.51 / % possible all: 96.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (23-JAN-2024)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACT3.28 (Apr. 15, 2021)data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.985→42.63 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.89 / SU R Cruickshank DPI: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.227 / SU Rfree Blow DPI: 0.18 / SU Rfree Cruickshank DPI: 0.171
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 1117 5 %RANDOM
Rwork0.1923 ---
obs0.1947 22338 99.3 %-
Displacement parametersBiso max: 159.52 Å2 / Biso mean: 20.39 Å2 / Biso min: 8.55 Å2
Baniso -1Baniso -2Baniso -3
1-4.2379 Å20 Å21.6368 Å2
2--2.1124 Å20 Å2
3----6.3502 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: final / Resolution: 1.985→42.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 186 358 2920
Biso mean--59.32 28.1 -
Num. residues----330
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d734SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes412HARMONIC5
X-RAY DIFFRACTIONt_it2578HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion357SEMIHARMONIC5
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_contact2682SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2578HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg3487HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion3.77
X-RAY DIFFRACTIONt_other_torsion13.3
LS refinement shellResolution: 1.99→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2607 22 4.92 %
Rwork0.222 425 -
all0.2243 447 -
obs--83.15 %

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