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- PDB-1qfm: PROLYL OLIGOPEPTIDASE FROM PORCINE MUSCLE -

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Basic information

Entry
Database: PDB / ID: 1qfm
TitlePROLYL OLIGOPEPTIDASE FROM PORCINE MUSCLE
ComponentsPROTEIN (PROLYL OLIGOPEPTIDASE)
KeywordsHYDROLASE / PROLYL OLIGOPEPTIDASE / AMNESIA / ALPHA/BETA-HYDROLASE / BETA-PROPELLER
Function / homology
Function and homology information


prolyl oligopeptidase / oligopeptidase activity / serine-type endopeptidase activity / proteolysis / cytoplasm / 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
1-HYDROXY-1-THIO-GLYCEROL / MONOTHIOGLYCEROL / Prolyl endopeptidase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.4 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 12, 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: Non-polymer description / Version format compliance
Revision 1.3Sep 14, 2011Group: Other
Revision 1.4Nov 12, 2014Group: Non-polymer description
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: PROTEIN (PROLYL OLIGOPEPTIDASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8099
Polymers80,9761
Non-polymers8338
Water15,979887
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.700, 99.600, 110.600
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: 80976.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: PORCINE BRAIN SEQUENCE WAS USED FOR STRUCTURE DETERMINATION AND REFINEMENT
Source: (natural) Sus scrofa (pig) / Cellular location: CYTOPLASM / Tissue: MUSCLE / References: UniProt: P23687, prolyl oligopeptidase
#2: Chemical ChemComp-SGL / 1-HYDROXY-1-THIO-GLYCEROL


Mass: 124.159 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3S
#3: Chemical ChemComp-SGM / MONOTHIOGLYCEROL


Mass: 108.159 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2S
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 887 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details1-THIOXY-GLYCEROL (SGL781) IS COVALENTLY BOUND TO SER554 MONOTHIOGLYCEROL IS COVALENTLY BOUND TO ...1-THIOXY-GLYCEROL (SGL781) IS COVALENTLY BOUND TO SER554 MONOTHIOGLYCEROL IS COVALENTLY BOUND TO CYS78 AND CYS532
Sequence detailsCYS25, CYS57 AND CYS255 ARE OXIDIZED WITH ONE OXYGEN ATOM. CYS175 AND CYS601 ARE OXIDIZED WITH TWO ...CYS25, CYS57 AND CYS255 ARE OXIDIZED WITH ONE OXYGEN ATOM. CYS175 AND CYS601 ARE OXIDIZED WITH TWO OXYGEN ATOMS.

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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
*PLUS
Density % sol: 48 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.5 / 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: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1997 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 140350 / % possible obs: 91 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 16.4
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.324 / % possible all: 80
Reflection
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 30 Å / % possible obs: 91 % / Num. measured all: 366752

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
SHARPphasing
X-PLOR3.851refinement
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 1.4→30 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.206 5631 4 %RANDOM
Rwork0.19 ---
obs-139056 91 %-
Displacement parametersBiso mean: 13.5 Å2
Refinement stepCycle: LAST / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5708 0 50 887 6645
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
Highest resolution: 1.4 Å / Lowest resolution: 30 Å / Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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