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- PDB-7vgc: Crystal structure of prolyl oligopeptidase from Microbulbifer are... -

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Basic information

Entry
Database: PDB / ID: 7vgc
TitleCrystal structure of prolyl oligopeptidase from Microbulbifer arenaceous complex with a transition state analog inhibitor ZPR
Componentsprolyl oligopeptidase
KeywordsHYDROLASE / S9A / prolyl endopeptidase / serine protease / mental disorder / amnesia
Function / homologyZ-PRO-PROLINAL / N-BENZYLOXYCARBONYL-L-PROLYL-L-PROLINAL
Function and homology information
Biological speciesMicrobulbifer arenaceous (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.722 Å
AuthorsHuang, P. / Yang, S.Q. / Jiang, Z.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: The structure and molecular dynamics of prolyl oligopeptidase from Microbulbifer arenaceous provide insights into catalytic and regulatory mechanisms.
Authors: Huang, P. / Lv, A. / Yan, Q. / Jiang, Z. / Yang, S.
History
DepositionSep 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.3Oct 30, 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 oligopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3534
Polymers79,9521
Non-polymers4013
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-7 kcal/mol
Surface area25080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.108, 65.622, 91.765
Angle α, β, γ (deg.)90.000, 105.290, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein prolyl oligopeptidase


Mass: 79952.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microbulbifer arenaceous (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: 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 / Feature type: SUBJECT OF INVESTIGATION / References: Z-PRO-PROLINAL
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.04M MES monohydrate pH 6.0, 8.8% (v/v) Polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Jun 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.722→30.96 Å / Num. obs: 18620 / % possible obs: 96.28 % / Redundancy: 5.1 % / CC1/2: 0.924 / CC star: 0.98 / Net I/σ(I): 5.75
Reflection shellResolution: 2.722→2.82 Å / Num. unique obs: 6850 / CC1/2: 0.924

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VGB

7vgb


Resolution: 2.722→30.96 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.873 / SU B: 18.113 / SU ML: 0.352 / Cross valid method: FREE R-VALUE / ESU R Free: 0.425 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2708 931 5 %
Rwork0.1952 17690 -
all0.199 --
obs-18608 96.352 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 44.608 Å2
Baniso -1Baniso -2Baniso -3
1--0.225 Å2-0 Å2-0.984 Å2
2---0.297 Å20 Å2
3---0.922 Å2
Refinement stepCycle: LAST / Resolution: 2.722→30.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5439 0 26 67 5532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0125619
X-RAY DIFFRACTIONr_angle_refined_deg1.2421.6397633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9235679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72322.792308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.20115853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8861528
X-RAY DIFFRACTIONr_chiral_restr0.1010.2691
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024403
X-RAY DIFFRACTIONr_nbd_refined0.2390.23400
X-RAY DIFFRACTIONr_nbtor_refined0.3240.23807
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2301
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2340.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2480.22
X-RAY DIFFRACTIONr_mcbond_it2.6934.4082719
X-RAY DIFFRACTIONr_mcangle_it4.3116.6123397
X-RAY DIFFRACTIONr_scbond_it2.814.52900
X-RAY DIFFRACTIONr_scangle_it4.2516.6764236
X-RAY DIFFRACTIONr_lrange_it6.89360.4569410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.722-2.7920.372650.309984X-RAY DIFFRACTION74.45
2.792-2.8690.384580.2951246X-RAY DIFFRACTION93.4097
2.869-2.9520.412580.2711242X-RAY DIFFRACTION97.3783
2.952-3.0430.282570.2361229X-RAY DIFFRACTION98.6196
3.043-3.1420.282620.2361194X-RAY DIFFRACTION98.9756
3.142-3.2530.274650.2161150X-RAY DIFFRACTION98.1422
3.253-3.3750.337650.2251062X-RAY DIFFRACTION97.745
3.375-3.5130.323520.2131063X-RAY DIFFRACTION96.7882
3.513-3.6690.285590.2061027X-RAY DIFFRACTION98.5481
3.669-3.8470.271450.179996X-RAY DIFFRACTION99.904
3.847-4.0550.246500.175932X-RAY DIFFRACTION99.4934
4.055-4.30.241470.149905X-RAY DIFFRACTION99.6859
4.3-4.5970.147430.143830X-RAY DIFFRACTION99.4305
4.597-4.9640.263460.147791X-RAY DIFFRACTION99.4062
4.964-5.4360.286420.172720X-RAY DIFFRACTION99.6078
5.436-6.0750.381340.188662X-RAY DIFFRACTION99.8565
6.075-7.0090.256300.186566X-RAY DIFFRACTION95.6661
7.009-8.5710.125240.125492X-RAY DIFFRACTION99.8066
8.571-12.0640.177190.145391X-RAY DIFFRACTION98.3213
12.064-30.960.338100.318208X-RAY DIFFRACTION88.9796

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