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- PDB-1h2y: PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, Y473F MUTANT WITH COVAL... -

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Basic information

Entry
Database: PDB / ID: 1h2y
TitlePROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, Y473F MUTANT WITH COVALENTLY BOUND INHIBITOR Z-PRO-PROLINAL
ComponentsPROLYL ENDOPEPTIDASE
KeywordsHYDROLASE / PROLYL OLIGOPEPTIDASE / AMNESIA / ALPHA/ BETA- HYDROLASE / BETA-PROPELLER / SERINE PROTEASE
Function / homology
Function and homology information


prolyl oligopeptidase / oligopeptidase activity / serine-type endopeptidase activity / proteolysis / cytosol
Similarity search - Function
Prolyl oligopeptidase, N-terminal domain / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / 7 Propeller / Methylamine Dehydrogenase; Chain H ...Prolyl oligopeptidase, N-terminal domain / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / 7 Propeller / Methylamine Dehydrogenase; Chain H / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Z-PRO-PROLINAL / N-BENZYLOXYCARBONYL-L-PROLYL-L-PROLINAL / Prolyl endopeptidase
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsRea, D. / Fulop, V.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Electrostatic Effects and Binding Determinants in the Catalysis of Prolyl Oligopeptidase: Site Specific Mutagenesis at the Oxyanion Binding Site
Authors: Szeltner, Z. / Rea, D. / Renner, V. / Fulop, V. / Polgar, L.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Structures of Prolyl Oligopeptidase Substrate/ Inhibitor Complexes. Use of Inhibitor Binding for Titration of the Catalytic Histidine Residue
Authors: Fulop, V. / Szeltner, Z. / Renner, V. / Polgar, L.
#2: Journal: Embo Rep. / Year: 2000
Title: Catalysis of Serine Oligopeptidases is Controlled by a Gating Filter Mechanism
Authors: Fulop, V. / Szeltner, Z. / Polgar, L.
#3: Journal: Cell(Cambridge,Mass.) / Year: 1998
Title: Prolyl Oligopeptidase: An Unusual Beta-Propeller Domain Regulates Proteolysis
Authors: Fulop, V. / Bocskei, Z. / Polgar, L.
History
DepositionAug 20, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2002Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2011Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Source and taxonomy / Version format compliance
Revision 1.2Mar 6, 2013Group: Other
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: PROLYL ENDOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6397
Polymers80,8481
Non-polymers7916
Water14,070781
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.800, 99.600, 110.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROLYL ENDOPEPTIDASE / / POST-PROLINE CLEAVING ENZYME / PE


Mass: 80848.344 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ENGINEERED MUTATION TYR 473 PHE / Source: (gene. exp.) SUS SCROFA (pig) / Tissue: BRAIN / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P23687, prolyl oligopeptidase
#2: Chemical ChemComp-ZPR / N-BENZYLOXYCARBONYL-L-PROLYL-L-PROLINAL / Z-PRO-PROLINAL


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 330.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22N2O4 / References: Z-PRO-PROLINAL
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 781 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCLEAVES PEPTIDE BONDS ON THE C-TERMINAL SIDE OF PROLYL RESIDUES WITHIN PEPTIDES OF UP TO ...CLEAVES PEPTIDE BONDS ON THE C-TERMINAL SIDE OF PROLYL RESIDUES WITHIN PEPTIDES OF UP TO APPROXIMATELY 30 AMINO ACIDS IN LENGTH. BELONGS TO PEPTIDASE FAMILY S9A. CHAIN A ENGINEERED MUTATION TYR 473 PHE

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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: 2.5 Å3/Da / Density % sol: 44 %
Crystal growpH: 8.5 / Details: SEE REFERENCE 3, pH 8.50
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Fulop, V., (1998) Cell, 94, 161.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
117 %(w/v)mPEG50001reservoir
215 %(v/v)glycerol1reservoir
31 %(v/v)monothioglycerol1reservoir
420 mM1reservoirCa(Ac)2
5100 mMTris1reservoir
610 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2002 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.78→33 Å / Num. obs: 75584 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 19.7
Reflection shellResolution: 1.78→1.84 Å / Redundancy: 4 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2.1 / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 33 Å / Num. measured all: 304631

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
X-PLORphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QFM

1qfm


Resolution: 1.78→33 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.194 3055 4 %RANDOM
Rwork0.172 ---
obs0.172 74318 99.7 %-
Displacement parametersBiso mean: 19.6 Å2
Refine analyzeLuzzati sigma a obs: 0.12 Å
Refinement stepCycle: LAST / Resolution: 1.78→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5700 0 54 781 6535
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
% reflection Rfree: 4 % / Rfactor all: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS

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