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- PDB-8wkb: Durio zibethinus trypsin inhibitor DzTI-7 -

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Basic information

Entry
Database: PDB / ID: 8wkb
TitleDurio zibethinus trypsin inhibitor DzTI-7
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 / 21 kDa seed protein-like
Function and homology information
Biological speciesDurio zibethinus (durian)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.35 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 27, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 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

Downloads & links

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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
D: 21 kDa seed protein-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,58922
Polymers85,2434
Non-polymers1,34618
Water7,999444
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)101.242, 102.680, 116.922
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: 21310.787 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: OR361617 / Source: (gene. exp.) Durio zibethinus (durian) / Strain: Chanee / Gene: LOC111287850 / Plasmid: pET32b / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 / References: UniProt: A0A6P5Y1F9
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / 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: 3.5 Å3/Da / Density % sol: 64.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris-HCl, 80 mM sodium chloride, 80 mM calcium chloride, 6% PEG 8,000, 8% glycerol

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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: 2.35→29.68 Å / Num. obs: 51452 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 46.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.038 / Rrim(I) all: 0.101 / Χ2: 0.93 / Net I/σ(I): 16.2
Reflection shellResolution: 2.35→2.42 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.261 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4381 / CC1/2: 0.925 / Rpim(I) all: 0.496 / Rrim(I) all: 1.357 / Χ2: 0.86 / % possible all: 99.7

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Processing

Software
NameVersionClassification
XDSJan 10, 2022 BUILT=20220110data reduction
Aimless0.7.9data scaling
PHENIX1.20.1_4487refinement
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.35→29.68 Å / SU ML: 0.3028 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.6975
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2417 2591 5.06 %
Rwork0.1924 48650 -
obs0.1949 51241 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.74 Å2
Refinement stepCycle: LAST / Resolution: 2.35→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5650 0 78 444 6172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00775859
X-RAY DIFFRACTIONf_angle_d0.90237955
X-RAY DIFFRACTIONf_chiral_restr0.0553856
X-RAY DIFFRACTIONf_plane_restr0.0081034
X-RAY DIFFRACTIONf_dihedral_angle_d16.48432088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.390.33741500.26132512X-RAY DIFFRACTION99
2.39-2.440.34091300.25152504X-RAY DIFFRACTION99.25
2.44-2.490.321120.24272551X-RAY DIFFRACTION99.4
2.49-2.540.33851200.23772534X-RAY DIFFRACTION99.21
2.54-2.60.30461320.24572513X-RAY DIFFRACTION99.59
2.6-2.670.33291230.23832550X-RAY DIFFRACTION99.66
2.67-2.740.29121290.21892531X-RAY DIFFRACTION99.77
2.74-2.820.27731430.21712534X-RAY DIFFRACTION99.85
2.82-2.910.30271080.21432562X-RAY DIFFRACTION99.66
2.91-3.010.2681710.21052498X-RAY DIFFRACTION99.78
3.01-3.130.27481620.2082541X-RAY DIFFRACTION99.7
3.13-3.280.27251500.20122552X-RAY DIFFRACTION99.89
3.28-3.450.22291360.18832563X-RAY DIFFRACTION99.93
3.45-3.670.28051160.20392574X-RAY DIFFRACTION99.59
3.67-3.950.26711260.18592577X-RAY DIFFRACTION99.59
3.95-4.340.20551270.15672590X-RAY DIFFRACTION99.96
4.34-4.970.16251450.14742592X-RAY DIFFRACTION99.89
4.97-6.250.19951410.16882646X-RAY DIFFRACTION100
6.26-29.680.23351700.20552726X-RAY DIFFRACTION99.83

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