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- PDB-2vs2: Neutron diffraction structure of endothiapepsin in complex with a... -

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Basic information

Entry
Database: PDB / ID: 2vs2
TitleNeutron diffraction structure of endothiapepsin in complex with a gem- diol inhibitor.
ComponentsENDOTHIAPEPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ACID PROTEINASE / ASPARTYL PROTEASE / ZYMOGEN / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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
GEM-DIOL INHIBITOR PD-135.040 / Chem-0QS / DEUTERATED WATER / Endothiapepsin
Similarity search - Component
Biological speciesCRYPHONECTRIA PARASITICA (chestnut blight fungus)
MethodNEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCoates, L. / Tuan, H.-F. / Tomanicek, S. / Kovalevsky, A. / Mustyakimov, M. / Erskine, P. / Cooper, J.
Citation
Journal: J.Am.Chem.Soc. / Year: 2008
Title: The Catalytic Mechanism of an Aspartic Proteinase Explored with Neutron and X-Ray Diffraction
Authors: Coates, L. / Tuan, H.-F. / Tomanicek, S. / Kovalevsky, A. / Mustyakimov, M. / Erskine, P. / Cooper, J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Preliminary Neutron and Ultrahigh-Resolution X-Ray Diffraction Studies of the Aspartic Proteinase Endothiapepsin Cocrystallized with a Gem-Diol Inhibitor.
Authors: Tuan, H.-F. / Erskine, P. / Langan, P. / Cooper, J. / Coates, L.
History
DepositionApr 17, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Mar 6, 2013Group: Other
Revision 1.3Sep 25, 2013Group: Database references / Other
Revision 1.4Jul 16, 2014Group: Advisory / Other / Structure summary
Revision 1.5Mar 22, 2017Group: Data collection
Revision 1.6Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.7Nov 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site ..._diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.pdbx_wavelength_list / _diffrn_source.source / _diffrn_source.type
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_validate_rmsd_angle / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_alt_id / _atom_site.label_atom_id / _atom_site.occupancy / _atom_site.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)34,5812
Polymers33,7961
Non-polymers7851
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)43.030, 75.720, 42.970
Angle α, β, γ (deg.)90.00, 97.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENDOTHIAPEPSIN / ASPARTATE PROTEASE


Mass: 33795.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ENDOTHIA PARASITICA FORMULA WEIGHT 33814.2
Source: (natural) CRYPHONECTRIA PARASITICA (chestnut blight fungus)
References: UniProt: P11838, endothiapepsin
#2: Chemical ChemComp-0QS / N~2~-[(2R)-2-benzyl-3-(tert-butylsulfonyl)propanoyl]-N-{(1R)-1-(cyclohexylmethyl)-3,3-difluoro-2,2-dihydroxy-4-[(2-morpholin-4-ylethyl)amino]-4-oxobutyl}-3-(1H-imidazol-3-ium-4-yl)-L-alaninamide / PD-135,040


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 784.934 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H56F2N7O8S / References: GEM-DIOL INHIBITOR PD-135.040
#3: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDescription: NONE
Crystal growpH: 4.6 / Details: PH 4.6

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SPALLATION SOURCE / Site: ORNL Spallation Neutron Source / Beamline: MANDI / Wavelength: 1 / Wavelength: 1 Å
DetectorType: BROOKHAVEN NATIONAL LAB / Detector: HELIUM-FREE / Date: Aug 1, 2007
RadiationScattering type: neutron
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→42.72 Å / Num. obs: 15780 / % possible obs: 85.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.268 / Rsym value: 0.268 / Net I/σ(I): 2.5
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 1.7 / % possible all: 73.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF TARGET
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1032 5.6 %RANDOM
Rwork0.219 ---
obs0.219 15766 --
Solvent computationSolvent model: BULK SOLVENT / Bsol: 33.67 Å2 / ksol: 0.62 e/Å3
Displacement parametersBiso mean: 11.41 Å2
Baniso -1Baniso -2Baniso -3
1-3.288 Å20 Å20.399 Å2
2--4.4 Å20 Å2
3---1.931 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 0 54 220 2662
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONc_bond_d0.006
NEUTRON DIFFRACTIONc_bond_d_na
NEUTRON DIFFRACTIONc_bond_d_prot
NEUTRON DIFFRACTIONc_angle_d
NEUTRON DIFFRACTIONc_angle_d_na
NEUTRON DIFFRACTIONc_angle_d_prot
NEUTRON DIFFRACTIONc_angle_deg1.05
NEUTRON DIFFRACTIONc_angle_deg_na
NEUTRON DIFFRACTIONc_angle_deg_prot
NEUTRON DIFFRACTIONc_dihedral_angle_d15.37
NEUTRON DIFFRACTIONc_dihedral_angle_d_na
NEUTRON DIFFRACTIONc_dihedral_angle_d_prot
NEUTRON DIFFRACTIONc_improper_angle_d0.88
NEUTRON DIFFRACTIONc_improper_angle_d_na
NEUTRON DIFFRACTIONc_improper_angle_d_prot
NEUTRON DIFFRACTIONc_mcbond_it
NEUTRON DIFFRACTIONc_mcangle_it
NEUTRON DIFFRACTIONc_scbond_it
NEUTRON DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.07 Å / Total num. of bins used: 10 /
Rfactor% reflection
Rfree0.345 12.3 %
Rwork0.352 -
obs-72 %

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