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- PDB-1qfs: PROLYL OLIGOPEPTIDASE FROM PORCINE MUSCLE WITH COVALENTLY BOUND I... -

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Basic information

Entry
Database: PDB / ID: 1qfs
TitlePROLYL OLIGOPEPTIDASE FROM PORCINE MUSCLE WITH COVALENTLY BOUND INHIBITOR Z-PRO-PROLINAL
ComponentsPROTEIN (PROLYL OLIGOPEPTIDASE)
KeywordsHYDROLASE / PROLYL OLIGOPEPTIDASE / AMNESIA / ALPHA/BETA-HYDROLASE / BETA-PROPELLER
Function / homology
Function and homology information


prolyl oligopeptidase / serine-type endopeptidase activity / proteolysis / cytoplasm
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 ...: / 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 / OTHER / Resolution: 2 Å
AuthorsFulop, V.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1998
Title: Prolyl oligopeptidase: an unusual beta-propeller domain regulates proteolysis.
Authors: Fulop, V. / Bocskei, Z. / Polgar, L.
History
DepositionApr 13, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0May 13, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 27, 2013Group: Other
Revision 1.4Aug 16, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (PROLYL OLIGOPEPTIDASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1952
Polymers80,8641
Non-polymers3301
Water13,241735
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.900, 99.800, 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 PROTEIN (PROLYL OLIGOPEPTIDASE) / PROLYL ENDOPEPTIDASE / POST-PROLINE CLEAVING ENZYME


Mass: 80864.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: PORCINE BRAIN SEQUENCE WAS USED FOR STRUCTURE REFINEMENT
Source: (natural) Sus scrofa (pig) / Cellular location: CYTOPLASM / Tissue: MUSCLE / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsZ-PRO-PROLINAL FORMS A HEMIACETAL ADDUCT WITH SER554

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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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growpH: 8.5 / Details: SEE REFERENCE, pH 8.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9096
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1997 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9096 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 51602 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 11.3
Reflection shellResolution: 2→2.06 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.449 / % possible all: 92
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 135322

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Processing

Software
NameVersionClassification
CCP4model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: OTHER
Starting model: 1QFM

1qfm


Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2118 4 %RANDOM
Rwork0.201 ---
obs-50498 95 %-
Displacement parametersBiso mean: 31.3 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5701 0 24 735 6460
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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
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
Rfactor obs: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS

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