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- PDB-7vgb: Crystal structure of apo prolyl oligopeptidase from Microbulbifer... -

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Basic information

Entry
Database: PDB / ID: 7vgb
TitleCrystal structure of apo prolyl oligopeptidase from Microbulbifer arenaceous
Componentsprolyl oligopeptidase
KeywordsHYDROLASE / S9A / prolyl endopeptidase / serine protease / mental disorder / amnesia
Function / homologyIMIDAZOLE / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / trimethylamine oxide
Function and homology information
Biological speciesMicrobulbifer arenaceous (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.227 Å
AuthorsHuang, P. / 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 1.3Nov 13, 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
B: prolyl oligopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,58720
Polymers159,9042
Non-polymers1,68218
Water18,3031016
1
A: prolyl oligopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,07213
Polymers79,9521
Non-polymers1,12012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-10 kcal/mol
Surface area26980 Å2
MethodPISA
2
B: prolyl oligopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5147
Polymers79,9521
Non-polymers5626
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area27320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.390, 125.395, 89.848
Angle α, β, γ (deg.)90.000, 96.837, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein prolyl oligopeptidase


Mass: 79952.180 Da / Num. of mol.: 2
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

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Non-polymers , 7 types, 1034 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#7: Chemical ChemComp-TMO / trimethylamine oxide


Mass: 75.110 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H9NO / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1016 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.19 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Trimethylamine N-oxide dihydrate, 0.1M Tris pH 8.5, 20% (w/v) Polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.227→44.198 Å / Num. obs: 64538 / % possible obs: 99.86 % / Redundancy: 6.8 % / Biso Wilson estimate: 19.9 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.1398 / Rpim(I) all: 0.0581 / Rrim(I) all: 0.1516 / Net I/σ(I): 12.53
Reflection shellResolution: 2.227→2.31 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.5265 / Mean I/σ(I) obs: 4.37 / Num. unique obs: 40296 / CC1/2: 0.899 / CC star: 0.973 / Rpim(I) all: 0.2292 / Rrim(I) all: 0.5753 / % possible all: 99.97

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MUN

3mun


Resolution: 2.227→44.198 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.865 / SU ML: 0.145 / Cross valid method: FREE R-VALUE / ESU R: 0.327 / ESU R Free: 0.208 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2072 3237 5.001 %
Rwork0.1524 61486 -
all0.155 --
obs-64531 99.744 %
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: 21.548 Å2
Baniso -1Baniso -2Baniso -3
1-1.048 Å20 Å2-1.486 Å2
2---0.767 Å2-0 Å2
3---0.073 Å2
Refinement stepCycle: LAST / Resolution: 2.227→44.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10892 0 105 1016 12013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01211286
X-RAY DIFFRACTIONr_angle_refined_deg1.431.63815308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.20951360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.322.876612
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65151788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4291556
X-RAY DIFFRACTIONr_chiral_restr0.1110.21380
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028760
X-RAY DIFFRACTIONr_nbd_refined0.2020.24960
X-RAY DIFFRACTIONr_nbtor_refined0.3130.27594
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2982
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2030.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1710.225
X-RAY DIFFRACTIONr_mcbond_it1.5471.9545450
X-RAY DIFFRACTIONr_mcangle_it2.4512.9226804
X-RAY DIFFRACTIONr_scbond_it2.3152.2125836
X-RAY DIFFRACTIONr_scangle_it3.5823.1948504
X-RAY DIFFRACTIONr_lrange_it5.37326.56217419
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.227-2.2850.2452350.244480.20347760.9010.90598.05280.176
2.285-2.3470.2562320.17944090.18346410.9010.9231000.16
2.347-2.4150.2562280.18143330.18545620.910.92299.97810.16
2.415-2.4890.2732190.18541730.1943930.8860.91199.97720.163
2.489-2.5710.2632130.16440330.16942460.9140.9361000.144
2.571-2.6610.2072040.15238910.15540950.9370.9481000.134
2.661-2.7610.2252000.16537940.16839940.9310.9421000.144
2.761-2.8730.2451920.16536420.16938360.9120.93999.94790.147
2.873-30.2321840.16735100.1737020.9260.94299.78390.151
3-3.1460.2391750.16233100.16634910.9270.94699.82810.148
3.146-3.3150.1861680.14631890.14833660.950.9699.73260.135
3.315-3.5150.1861570.14129940.14331550.9560.96799.87320.132
3.515-3.7560.1871490.14328390.14529920.9540.96499.86630.137
3.756-4.0540.1561390.12826390.12927800.9680.97299.92810.125
4.054-4.4380.1731280.12324200.12525490.970.97799.96080.123
4.438-4.9550.1551170.12122180.12323370.9680.97599.91440.125
4.955-5.710.1811020.12919460.13220480.9690.9751000.13
5.71-6.9640.188870.15616580.15817450.960.9671000.158
6.964-9.7290.179680.1412950.14213630.9640.9711000.148
9.729-44.1980.196400.1717450.1738080.9510.95697.15350.185

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