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- PDB-1oew: ATOMIC RESOLUTION STRUCTURE OF NATIVE ENDOTHIAPEPSIN -

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Basic information

Entry
Database: PDB / ID: 1oew
TitleATOMIC RESOLUTION STRUCTURE OF NATIVE ENDOTHIAPEPSIN
ComponentsENDOTHIAPEPSIN
KeywordsHYDROLASE / ASPARTIC PROTEINASE MECHANISM / ATOMIC RESOLUTION / SUCCINIMIDE / ANISOTROPIC REFINEMENT
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
SERINE / THREONINE / Endothiapepsin
Similarity search - Component
Biological speciesCRYPHONECTRIA PARASITICA (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 0.9 Å
AuthorsCoates, L. / Erskine, P.T. / Mall, S. / Gill, R.S. / Wood, S.P. / Myles, D.A.A. / Cooper, J.B.
CitationJournal: Protein Sci. / Year: 2003
Title: Atomic Resolution Analysis of the Catalytic Site of an Aspartic Proteinase and an Unexpected Mode of Binding by Short Peptides
Authors: Erskine, P.T. / Coates, L. / Mall, S. / Gill, R.S. / Wood, S.P. / Myles, D.A.A. / Cooper, J.B.
History
DepositionMar 31, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 20, 2018Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_validate_rmsd_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _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)34,5929
Polymers33,7961
Non-polymers7978
Water10,971609
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.720, 74.660, 42.550
Angle α, β, γ (deg.)90.00, 97.27, 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 / EAPA / EPN-1


Mass: 33795.840 Da / Num. of mol.: 1 / Fragment: RESIDUES 90-419 / Source method: isolated from a natural source
Details: SHORT PEPTIDE (MODELLED AS SER-THR) BOUND NON-COVALENTLY IN THE ACTIVE SITE CLEFT
Source: (natural) CRYPHONECTRIA PARASITICA (chestnut blight fungus)
References: UniProt: P11838, endothiapepsin

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Non-polymers , 5 types, 617 molecules

#2: Chemical ChemComp-SER / SERINE / Serine


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#3: Chemical ChemComp-THR / THREONINE / Threonine


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO3
#4: 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
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 609 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCATALYSES THE HYDROLYSIS OF PROTEINS WITH BROAD SPECIFICITY THE ACTIVITY OF THIS PROTEIN IS SIMILAR ...CATALYSES THE HYDROLYSIS OF PROTEINS WITH BROAD SPECIFICITY THE ACTIVITY OF THIS PROTEIN IS SIMILAR TO PEPSIN A, SINCE IT PREFERS HYDROPHOBIC RESIDUES AT P1 AND P1'. ALSO HAS THE ABILITY TO CLOT MILK.
Sequence detailsASP A54 AND GLY A55 HAVE CYCLISED TO FORM A SUCCINIMIDE

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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: 1.99 Å3/Da / Density % sol: 38 %
Crystal growpH: 4.6
Details: BATCH METHOD WITH ENZYME AT A CONCENTRATION OF 2 MG/ML IN 100 MM SODIUM ACETATE BUFFER AT PH 4.6 (MOEWS AND BUNN, 1970) CRYSTALS LEFT TO GROW FOLLOWING SLOW ADDITION OF AMMONIUM SULPHATE TO ...Details: BATCH METHOD WITH ENZYME AT A CONCENTRATION OF 2 MG/ML IN 100 MM SODIUM ACETATE BUFFER AT PH 4.6 (MOEWS AND BUNN, 1970) CRYSTALS LEFT TO GROW FOLLOWING SLOW ADDITION OF AMMONIUM SULPHATE TO FINAL CONCENTRATION OF 0.35 G/ML (55% SATURATION).
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12 mg/mlprotein11
2100 mMsodium acetate11pH4.6
355 %satammonium sulfate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8439
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8439 Å / Relative weight: 1
ReflectionResolution: 0.91→42.3 Å / Num. obs: 186749 / % possible obs: 99.4 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 8.6
Reflection shellResolution: 0.91→0.96 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 3 / % possible all: 99.4
Reflection shell
*PLUS
% possible obs: 99.4 %

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Processing

Software
NameClassification
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: OTHER / Resolution: 0.9→100 Å / Num. parameters: 27802 / Num. restraintsaints: 34005 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.147 9383 5 %RANDOM
obs0.121 -99.4 %-
all-186749 --
Solvent computationSolvent model: MOEWS AND KRETSINGER
Refine analyzeNum. disordered residues: 34
Refinement stepCycle: LAST / Resolution: 0.9→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 0 45 609 3042
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.032
X-RAY DIFFRACTIONs_zero_chiral_vol0.085
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.1
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.121
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.03
X-RAY DIFFRACTIONs_approx_iso_adps0.081
Refinement
*PLUS
Highest resolution: 0.91 Å / Lowest resolution: 42.3 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.121
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.085
X-RAY DIFFRACTIONs_chiral_restr0.1

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