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- PDB-8wio: Durio zibethinus trypsin inhibitor DzTI-10 -

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Basic information

Entry
Database: PDB / ID: 8wio
TitleDurio zibethinus trypsin inhibitor DzTI-10
Components21 kDa seed protein-like
KeywordsPLANT PROTEIN / Kunitz-type trypsin inhibitor / seed protein / Durio zibethinus
Function / homologySoybean 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 / endopeptidase inhibitor activity / 21 kDa seed protein-like
Function and homology information
Biological speciesDurio zibethinus (durian)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsDeentanya, P. / Wangkanont, K.
Funding support Thailand, 3items
OrganizationGrant numberCountry
Other governmentNational Research Council of Thailand (NRCT), N42A650270 Thailand
Other governmentChulalongkorn University, RES_65_389_23_039 Thailand
Other governmentChulalongkorn University, CU_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 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,7746
Polymers64,4853
Non-polymers2883
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.162, 164.162, 64.675
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

#1: Protein 21 kDa seed protein-like


Mass: 21495.105 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: OR361614 / Source: (gene. exp.) Durio zibethinus (durian) / Strain: Chanee / Gene: LOC111287814 / Plasmid: pET32b / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 / References: UniProt: A0A6P5Y2I1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
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: 3.34 Å3/Da / Density % sol: 63.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 100 mM sodium acetate, 1 M ammonium sulfate

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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: Dec 12, 2021
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.7→29.59 Å / Num. obs: 9912 / % possible obs: 99.8 % / Redundancy: 14 % / Biso Wilson estimate: 167.38 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.033 / Rrim(I) all: 0.125 / Χ2: 0.95 / Net I/σ(I): 16
Reflection shellResolution: 3.7→4.14 Å / Redundancy: 14.6 % / Rmerge(I) obs: 1.371 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2748 / CC1/2: 0.866 / Rpim(I) all: 0.369 / Rrim(I) all: 1.421 / Χ2: 1.05 / % possible all: 100

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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: 3.7→29.59 Å / SU ML: 0.5207 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 40.9959
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3154 495 5.01 %
Rwork0.273 9392 -
obs0.2752 9887 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 182.47 Å2
Refinement stepCycle: LAST / Resolution: 3.7→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4266 0 15 0 4281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00364383
X-RAY DIFFRACTIONf_angle_d0.69555963
X-RAY DIFFRACTIONf_chiral_restr0.0495640
X-RAY DIFFRACTIONf_plane_restr0.0055775
X-RAY DIFFRACTIONf_dihedral_angle_d5.3911586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-4.070.43321220.35512291X-RAY DIFFRACTION99.96
4.07-4.660.48261100.3592320X-RAY DIFFRACTION99.96
4.66-5.860.34041180.31632335X-RAY DIFFRACTION100
5.86-29.590.26061450.21612446X-RAY DIFFRACTION99.88

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