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- PDB-3ivm: apPEP_WT+PP closed state -

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Basic information

Entry
Database: PDB / ID: 3ivm
TitleapPEP_WT+PP closed state
Componentsprolyl endopeptidase
KeywordsHydrolase/Hydrolase Inhibitor / prolyl endopeptidase / Hydrolase-Hydrolase Inhibitor complex
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 ...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 oligopeptidase
Similarity search - Component
Biological speciesAeromonas punctata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsChiu, T.K.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Induced-fit mechanism for prolyl endopeptidase
Authors: Li, M. / Chen, C. / Davies, D.R. / Chiu, T.K.
History
DepositionSep 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Structure summary
Revision 1.3Feb 27, 2013Group: Other
Revision 1.4Sep 6, 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_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 6, 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

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Assembly

Deposited unit
A: prolyl endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1113
Polymers77,4511
Non-polymers6612
Water8,953497
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.864, 93.630, 152.062
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsOne monomer per asu.

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Components

#1: Protein prolyl endopeptidase


Mass: 77450.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas punctata (bacteria) / Gene: prolyl endopeptidase / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X6R4
#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.: 2 / Source method: obtained synthetically / Formula: C18H22N2O4 / References: Z-PRO-PROLINAL
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAUTHORS STATE THAT THESE ARE NOT MUTATIONS, BUT ERROR IN DNA SEQUENCING OF THE ORIGINAL DEPOSITED ...AUTHORS STATE THAT THESE ARE NOT MUTATIONS, BUT ERROR IN DNA SEQUENCING OF THE ORIGINAL DEPOSITED FILE. THEY CONFIRMED THIS WITH DNA SEQUENCING

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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: 2.84 Å3/Da / Density % sol: 56.63 %
Crystal growTemperature: 287 K / Method: vapor diffusion / pH: 7.5
Details: 8mg/ml protein in 20mM Hepes (pH7.5), 100mM NaCl, 5% w/v glycerol, 1mM EDTA, and 1mM DTT. Equal volume of protein and precipitant (20mM MES (pH 6.5), 17% w/v PEG10K) were equilibrated by ...Details: 8mg/ml protein in 20mM Hepes (pH7.5), 100mM NaCl, 5% w/v glycerol, 1mM EDTA, and 1mM DTT. Equal volume of protein and precipitant (20mM MES (pH 6.5), 17% w/v PEG10K) were equilibrated by vapor diffusion at 14C. Crystals were soaked with the inhibitor ZPR. Cryosolution is precipitant plus 5% more PEG10K and 20% w/v glycerol, VAPOR DIFFUSION, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97934 Å
DetectorDetector: CCD / Date: Jul 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.05→40 Å / Num. all: 56780 / Num. obs: 55531 / % possible obs: 97.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 14.1 Å2 / Rsym value: 0.156 / Net I/σ(I): 10.7
Reflection shellResolution: 2.05→2.12 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 0.477

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Processing

Software
NameVersionClassification
HKL-2000data collection
EPMRphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3IUJ

3iuj


Resolution: 2.05→39.87 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2258519.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.271 5194 5.1 %RANDOM
Rwork0.222 ---
obs0.222 54688 95.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.099 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1--6.85 Å20 Å20 Å2
2--10.56 Å20 Å2
3----3.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.05→39.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5361 0 41 497 5899
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.471.5
X-RAY DIFFRACTIONc_mcangle_it4.142
X-RAY DIFFRACTIONc_scbond_it4.972
X-RAY DIFFRACTIONc_scangle_it6.12.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.05→2.12 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.349 449 4.8 %
Rwork0.303 8927 -
obs--87.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep_spp.paramprotein_spp.top
X-RAY DIFFRACTION2zppoh.paramzppoh.top

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