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- PDB-6jym: Crystal structure of Prolyl Endopeptidase from Haliotis discus hannai -

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Basic information

Entry
Database: PDB / ID: 6jym
TitleCrystal structure of Prolyl Endopeptidase from Haliotis discus hannai
ComponentsProlyl endopeptidase
KeywordsHYDROLASE / A serine protease subfamily
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis / cytoplasm
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
Prolyl endopeptidase
Similarity search - Component
Biological speciesHaliotis discus hannai (Japanese disc abalone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLi, W. / Cao, M. / Jin, T.
CitationJournal: FOOD CHEM / Year: 2020
Title: Characterization and crystal structure of prolyl endopeptidase from abalone (Haliotis discus hannai).
Authors: Li, W.Y. / Li, Y. / Chen, Y.L. / Hu, J.J. / Mengist, H.M. / Liu, G.M. / Jin, T. / Cao, M.J.
History
DepositionApr 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prolyl endopeptidase


Theoretical massNumber of molelcules
Total (without water)85,8801
Polymers85,8801
Non-polymers00
Water18,3031016
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area27420 Å2
Unit cell
Length a, b, c (Å)55.325, 104.955, 137.739
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 Prolyl endopeptidase /


Mass: 85880.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliotis discus hannai (Japanese disc abalone)
Gene: PREP / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A0A1X9T5X9, prolyl oligopeptidase
#2: Water ChemComp-HOH / water / Water


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

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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: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 20% PEG 3350 and 0.2 M ammonium citrate (dibasic)

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Data collection

DiffractionMean temperature: 190 K / Ambient temp details: Liquid nitrogen steam / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97894 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 22, 2018 / Details: silicon crystal (111) monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97894 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 125459 / % possible obs: 97.4 % / Redundancy: 12.6 % / Net I/σ(I): 21.42
Reflection shellResolution: 1.5→1.53 Å / CC1/2: 0.883

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QFS

1qfs


Resolution: 1.5→46.117 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.54
RfactorNum. reflection% reflection
Rfree0.1923 6269 5 %
Rwork0.1787 --
obs0.1794 125368 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→46.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5657 0 0 1016 6673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025884
X-RAY DIFFRACTIONf_angle_d0.4577980
X-RAY DIFFRACTIONf_dihedral_angle_d15.4433475
X-RAY DIFFRACTIONf_chiral_restr0.063836
X-RAY DIFFRACTIONf_plane_restr0.0031041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4999-1.5170.26081920.24673640X-RAY DIFFRACTION91
1.517-1.53480.22011980.23453786X-RAY DIFFRACTION93
1.5348-1.55360.22651990.22473765X-RAY DIFFRACTION94
1.5536-1.57320.24262010.22463826X-RAY DIFFRACTION94
1.5732-1.59390.22682010.21243803X-RAY DIFFRACTION94
1.5939-1.61580.22022020.21023839X-RAY DIFFRACTION95
1.6158-1.63880.22242040.20953877X-RAY DIFFRACTION95
1.6388-1.66330.22452030.2043869X-RAY DIFFRACTION96
1.6633-1.68930.22572030.20143859X-RAY DIFFRACTION96
1.6893-1.7170.21592080.20863948X-RAY DIFFRACTION97
1.717-1.74660.22782070.20163928X-RAY DIFFRACTION97
1.7466-1.77840.22272060.20623910X-RAY DIFFRACTION97
1.7784-1.81260.20872070.20393944X-RAY DIFFRACTION97
1.8126-1.84960.2322090.19643953X-RAY DIFFRACTION97
1.8496-1.88980.21942070.19433948X-RAY DIFFRACTION98
1.8898-1.93370.1942080.18443949X-RAY DIFFRACTION98
1.9337-1.98210.21212120.18024028X-RAY DIFFRACTION98
1.9821-2.03570.19962100.18253995X-RAY DIFFRACTION98
2.0357-2.09560.20532080.17173959X-RAY DIFFRACTION98
2.0956-2.16320.18782130.17694050X-RAY DIFFRACTION99
2.1632-2.24060.19332130.17684024X-RAY DIFFRACTION99
2.2406-2.33030.17872130.17854052X-RAY DIFFRACTION99
2.3303-2.43630.18982130.18034043X-RAY DIFFRACTION99
2.4363-2.56470.19392130.17954059X-RAY DIFFRACTION99
2.5647-2.72540.19972160.1824091X-RAY DIFFRACTION99
2.7254-2.93580.18282160.17914112X-RAY DIFFRACTION99
2.9358-3.23120.18842170.16094117X-RAY DIFFRACTION100
3.2312-3.69860.15822190.14994168X-RAY DIFFRACTION100
3.6986-4.65910.15982210.1464196X-RAY DIFFRACTION100
4.6591-46.13870.17622300.17954361X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 112.4328 Å / Origin y: 7.1332 Å / Origin z: 158.1781 Å
111213212223313233
T0.0965 Å2-0.004 Å20.0073 Å2-0.1108 Å20.0029 Å2--0.1087 Å2
L0.2138 °2-0.024 °20.0266 °2-0.4172 °20.012 °2--0.2773 °2
S0.0031 Å °0.0098 Å °0.0331 Å °-0.0184 Å °0.013 Å °-0.0276 Å °0.0025 Å °0.0039 Å °-0.0164 Å °
Refinement TLS groupSelection details: all

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