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- PDB-8wfo: Durio zibethinus trypsin inhibitor DzTI-4 -

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Basic information

Entry
Database: PDB / ID: 8wfo
TitleDurio zibethinus trypsin inhibitor DzTI-4
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 / metal ion binding / ACETATE ION / 21 kDa seed protein-like
Function and homology information
Biological speciesDurio zibethinus (durian)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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: 21 kDa seed protein-like
B: 21 kDa seed protein-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,41626
Polymers43,3472
Non-polymers2,06924
Water8,539474
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)53.500, 64.281, 128.404
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

#1: 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
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H2O
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: 2.59 Å3/Da / Density % sol: 52.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100 mM sodium acetate, 100 mM zinc acetate, 40% PEG 1,000

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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: Apr 23, 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: 1.55→29.65 Å / Num. obs: 65086 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 16.37 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.038 / Rrim(I) all: 0.101 / Χ2: 0.96 / Net I/σ(I): 11.4
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 7 % / Rmerge(I) obs: 0.905 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3207 / CC1/2: 0.869 / Rpim(I) all: 0.366 / Rrim(I) all: 0.978 / Χ2: 0.81 / % possible all: 99.9

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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: 1.55→29.65 Å / SU ML: 0.1573 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.7354
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2063 3289 5.06 %
Rwork0.1759 61665 -
obs0.1775 64954 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.97 Å2
Refinement stepCycle: LAST / Resolution: 1.55→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2998 0 78 474 3550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613242
X-RAY DIFFRACTIONf_angle_d0.85254400
X-RAY DIFFRACTIONf_chiral_restr0.0584478
X-RAY DIFFRACTIONf_plane_restr0.0076569
X-RAY DIFFRACTIONf_dihedral_angle_d16.6691194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.331480.27732654X-RAY DIFFRACTION99.72
1.57-1.60.28461440.24732624X-RAY DIFFRACTION99.78
1.6-1.620.2421260.23752656X-RAY DIFFRACTION99.86
1.62-1.650.2941350.23032646X-RAY DIFFRACTION99.78
1.65-1.680.26961270.22152663X-RAY DIFFRACTION99.96
1.68-1.710.24331400.20862665X-RAY DIFFRACTION99.93
1.71-1.750.23681400.19912637X-RAY DIFFRACTION99.75
1.75-1.790.21751560.19012681X-RAY DIFFRACTION99.86
1.79-1.830.22751520.17982608X-RAY DIFFRACTION99.82
1.83-1.870.19271460.17872641X-RAY DIFFRACTION99.79
1.87-1.930.21881420.18282666X-RAY DIFFRACTION99.68
1.93-1.980.21571400.1812682X-RAY DIFFRACTION99.82
1.98-2.050.2321620.17392647X-RAY DIFFRACTION99.79
2.05-2.120.21741330.17712647X-RAY DIFFRACTION99.75
2.12-2.20.20091450.17012680X-RAY DIFFRACTION99.72
2.2-2.30.20491550.16922662X-RAY DIFFRACTION99.82
2.3-2.430.19941450.17522692X-RAY DIFFRACTION99.75
2.43-2.580.22251560.17772674X-RAY DIFFRACTION99.65
2.58-2.780.19871510.1732683X-RAY DIFFRACTION99.75
2.78-3.060.19681270.16262729X-RAY DIFFRACTION99.9
3.06-3.50.18741210.15912766X-RAY DIFFRACTION99.93
3.5-4.40.16011350.14562776X-RAY DIFFRACTION99.93
4.4-29.650.19661630.18162886X-RAY DIFFRACTION99.77

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