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- PDB-1e8m: PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, MUTANT, COMPLEXED WITH ... -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1e8m
TitlePROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, MUTANT, COMPLEXED WITH INHIBITOR
ComponentsPROLYL ENDOPEPTIDASE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / PROLYL OLIGOPEPTIDASE / AMNESIA / ALPHA/ BETA-HYDROLASE / BETA-PROPELLER / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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
N-[(benzyloxy)carbonyl]glycyl-L-proline / N-[(benzyloxy)carbonyl]glycyl-L-proline / Prolyl endopeptidase
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsFulop, V.
Citation
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.
#1: Journal: Embo Rep. / Year: 2000
Title: Catalysis of Serine Oligopeptidases is Controlled by a Gating Filter Mechanism
Authors: Fulop, V. / Szeltner, Z. / Polgar, L.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1998
Title: Prolyl Oligopeptidase: An Unusual Beta-Propeller Domain Regulates Proteolysis
Authors: Fulop, V. / Bocskei, Z. / Polgar, L.
History
DepositionSep 27, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2001Provider: 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 1.2Nov 30, 2012Group: Other
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)81,2473
Polymers80,8481
Non-polymers3982
Water21,6721203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)71.100, 100.100, 111.300
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 / PROLYL ENDOPEPTIDASE / POST-PROLINE CLEAVING ENZYME


Mass: 80848.344 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SUS SCROFA (pig) / Tissue: BRAIN / Cellular location: CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P23687, prolyl oligopeptidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-P0H / N-[(benzyloxy)carbonyl]glycyl-L-proline


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 306.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18N2O5 / References: N-[(benzyloxy)carbonyl]glycyl-L-proline
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1203 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A CONTAINS ENGINEERED MUTATION S554A

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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 8.50
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Fulop, V., (1998) Cell(Cambridge,Mass.), 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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.909
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1999 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.909 Å / Relative weight: 1
ReflectionResolution: 1.5→18 Å / Num. obs: 124438 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 13.7 Å2 / Rsym value: 0.032 / Net I/σ(I): 36
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 8 / Rsym value: 0.128 / % possible all: 90.7
Reflection
*PLUS
Num. measured all: 470813 / Rmerge(I) obs: 0.032

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Processing

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

1qfm


Resolution: 1.5→18 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.217 5047 4 %RANDOM
Rwork0.193 ---
obs0.193 123471 94.9 %-
Displacement parametersBiso mean: 14.5 Å2
Refinement stepCycle: LAST / Resolution: 1.5→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5700 0 28 1203 6931
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
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.195 / Rfactor obs: 0.193 / Rfactor Rfree: 0.217 / Num. reflection all: 124438
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.5

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