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- PDB-7y1x: Crystal structure of prolyl oligopeptidase from Microbulbifer are... -

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Basic information

Entry
Database: PDB / ID: 7y1x
TitleCrystal structure of prolyl oligopeptidase from Microbulbifer arenaceous complex with PEG400 and MES
Componentsprolyl oligopeptidase
KeywordsHYDROLASE / S9A / prolyl endopeptidase / serine protease / mental disorder / amnesia
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesMicrobulbifer arenaceous (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsHuang, P. / Jiang, Z.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of prolyl oligopeptidase from Microbulbifer arenaceous complex with PEG400 and MES
Authors: Huang, P. / Jiang, Z.Q.
History
DepositionJun 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 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)81,99812
Polymers79,9521
Non-polymers2,04511
Water9,368520
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-16 kcal/mol
Surface area25010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.044, 65.065, 91.331
Angle α, β, γ (deg.)90.000, 104.948, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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(DE3) (bacteria) / References: prolyl oligopeptidase

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Non-polymers , 5 types, 531 molecules

#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / 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: 43.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.04 M 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: 0.97944 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: 0.97944 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. obs: 75931 / % possible obs: 94.38 % / Redundancy: 6.7 % / CC1/2: 0.998 / Net I/σ(I): 15.11
Reflection shellResolution: 1.67→1.7 Å / Num. unique obs: 7149 / CC1/2: 0.899

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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: 3MUN

3mun


Resolution: 1.67→31.651 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.705 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.095 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1887 3688 4.866 %
Rwork0.1598 72104 -
all0.161 --
obs-75792 94.38 %
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: 16.037 Å2
Baniso -1Baniso -2Baniso -3
1-0.035 Å2-0 Å20.021 Å2
2---0.128 Å20 Å2
3---0.071 Å2
Refinement stepCycle: LAST / Resolution: 1.67→31.651 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5414 0 128 520 6062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0125700
X-RAY DIFFRACTIONr_angle_refined_deg2.2221.6377726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2985678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16222.852305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3515890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8161528
X-RAY DIFFRACTIONr_chiral_restr0.130.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024365
X-RAY DIFFRACTIONr_nbd_refined0.2290.23958
X-RAY DIFFRACTIONr_nbtor_refined0.3510.24100
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2891
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.220.295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1790.228
X-RAY DIFFRACTIONr_mcbond_it1.4471.3312709
X-RAY DIFFRACTIONr_mcangle_it2.1571.9953385
X-RAY DIFFRACTIONr_scbond_it2.6371.662991
X-RAY DIFFRACTIONr_scangle_it3.8762.3644340
X-RAY DIFFRACTIONr_lrange_it5.04120.22410823
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.7130.2472530.1924997X-RAY DIFFRACTION88.8024
1.713-1.760.2352570.1815038X-RAY DIFFRACTION92.3278
1.76-1.8110.2112450.1715075X-RAY DIFFRACTION94.8645
1.811-1.8670.2072580.1614897X-RAY DIFFRACTION94.5525
1.867-1.9280.2242430.164696X-RAY DIFFRACTION94.1659
1.928-1.9960.1892350.1564493X-RAY DIFFRACTION92.0919
1.996-2.0710.1932270.1534241X-RAY DIFFRACTION90.3356
2.071-2.1560.2042050.1454332X-RAY DIFFRACTION95.9805
2.156-2.2520.1722040.1424186X-RAY DIFFRACTION96.6747
2.252-2.3610.1941910.1494035X-RAY DIFFRACTION96.9488
2.361-2.4890.1971960.1533803X-RAY DIFFRACTION96.7344
2.489-2.640.1892220.1563586X-RAY DIFFRACTION96.9203
2.64-2.8220.1831810.1633334X-RAY DIFFRACTION94.8718
2.822-3.0480.1851630.1633029X-RAY DIFFRACTION92.3344
3.048-3.3380.1611510.1592951X-RAY DIFFRACTION98.3201
3.338-3.7320.1631220.1532717X-RAY DIFFRACTION98.2693
3.732-4.3080.1641120.1522391X-RAY DIFFRACTION98.1184
4.308-5.2730.171080.1541935X-RAY DIFFRACTION94.8468
5.273-7.4440.231680.1911498X-RAY DIFFRACTION92.1719
7.444-31.6510.185470.211870X-RAY DIFFRACTION95.4214

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