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- PDB-8wk1: Bovine trypsin in complex with Durio zibethinus trypsin inhibitor... -

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Basic information

Entry
Database: PDB / ID: 8wk1
TitleBovine trypsin in complex with Durio zibethinus trypsin inhibitor DzTI-4
Components
  • 21 kDa seed protein-like
  • Cationic trypsin
KeywordsPLANT PROTEIN / Kunitz-type trypsin inhibitor / seed protein / Durio zibethinus / bovine trypsin
Function / homology
Function and homology information


endopeptidase inhibitor activity / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature. / Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / : / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family ...Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature. / Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / : / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
ACETATE ION / 21 kDa seed protein-like / Serine protease 1
Similarity search - Component
Biological speciesDurio zibethinus (durian)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDeentanya, P. / Wangkanont, K.
Funding support Thailand, 3items
OrganizationGrant numberCountry
National Research Council of Thailand (NRCT)N42A650270 Thailand
Chulalongkorn UniversityRES_65_389_23_039 Thailand
Chulalongkorn UniversityCU_GR_62_28_23_10 Thailand
CitationJournal: Protein Sci. / Year: 2024
Title: Kunitz-type trypsin inhibitor from durian (Durio zibethinus) employs a distinct loop for trypsin inhibition.
Authors: Deetanya, P. / Limsardsanakij, K. / Sabat, G. / Pattaradilokrat, S. / Chaisuekul, C. / Wangkanont, K.
History
DepositionSep 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Nov 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cationic trypsin
B: 21 kDa seed protein-like
C: Cationic trypsin
D: 21 kDa seed protein-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,57022
Polymers89,9954
Non-polymers1,57418
Water10,323573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Site-directed mutagenesis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.473, 72.055, 147.495
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00760, trypsin
#2: Protein 21 kDa seed protein-like


Mass: 21673.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Durio zibethinus (durian) / Strain: Chanee / Gene: LOC111287540 / Plasmid: pET32b / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 / References: UniProt: A0A6P5Y0F4

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Non-polymers , 4 types, 591 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 573 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.08 Å3/Da / Density % sol: 40.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100 mM sodium acetate, 200 mM ammonium sulfate, 25% PEG 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 17, 2022
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→29.76 Å / Num. obs: 51078 / % possible obs: 99.2 % / Redundancy: 7.4 % / Biso Wilson estimate: 28.12 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.045 / Rrim(I) all: 0.124 / Χ2: 0.98 / Net I/σ(I): 11.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.922 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3718 / CC1/2: 0.788 / Rpim(I) all: 0.356 / Rrim(I) all: 0.989 / Χ2: 1 / % possible all: 98.6

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Processing

Software
NameVersionClassification
XDSJan 10, 2022 BUILT=20220110data reduction
Aimless0.7.9data scaling
PHASER2.8.3phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.76 Å / SU ML: 0.2027 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.8928
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2244 2473 4.85 %
Rwork0.1774 48541 -
obs0.1797 51014 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.14 Å2
Refinement stepCycle: LAST / Resolution: 2→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6136 0 98 573 6807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00766346
X-RAY DIFFRACTIONf_angle_d0.96238598
X-RAY DIFFRACTIONf_chiral_restr0.0618943
X-RAY DIFFRACTIONf_plane_restr0.00621100
X-RAY DIFFRACTIONf_dihedral_angle_d15.94732256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.30261250.24532636X-RAY DIFFRACTION98.89
2.04-2.080.26211180.21912713X-RAY DIFFRACTION98.47
2.08-2.130.30521290.19882607X-RAY DIFFRACTION97.85
2.13-2.170.24921180.19452647X-RAY DIFFRACTION98.71
2.17-2.230.25161360.19342670X-RAY DIFFRACTION99.19
2.23-2.290.26821360.18432663X-RAY DIFFRACTION98.49
2.29-2.360.26741310.19122668X-RAY DIFFRACTION98.59
2.36-2.430.26651480.20062652X-RAY DIFFRACTION98.77
2.43-2.520.2421440.1982670X-RAY DIFFRACTION98.98
2.52-2.620.26731430.19362645X-RAY DIFFRACTION99.08
2.62-2.740.25541250.19482712X-RAY DIFFRACTION99.27
2.74-2.880.26131560.1832685X-RAY DIFFRACTION98.85
2.88-3.060.22081340.17862698X-RAY DIFFRACTION99.47
3.06-3.30.19861400.17662714X-RAY DIFFRACTION99.3
3.3-3.630.23871210.16742747X-RAY DIFFRACTION99.48
3.63-4.160.18631320.15052771X-RAY DIFFRACTION99.66
4.16-5.230.16991610.14692751X-RAY DIFFRACTION99.69
5.23-29.760.21671760.18382892X-RAY DIFFRACTION99.64

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