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- PDB-8whc: Durio zibethinus trypsin inhibitor DzTI-9 -

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Basic information

Entry
Database: PDB / ID: 8whc
TitleDurio zibethinus trypsin inhibitor DzTI-9
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 / ACETATE ION / 21 kDa seed protein-like
Function and homology information
Biological speciesDurio zibethinus (durian)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 23, 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
C: 21 kDa seed protein-like
D: 21 kDa seed protein-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,91819
Polymers86,7014
Non-polymers1,21615
Water12,953719
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)66.305, 70.413, 203.592
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: 21675.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: OR361615 / Source: (gene. exp.) Durio zibethinus (durian) / Strain: Chanee / Gene: LOC111287814 / Plasmid: pET32b / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 / Variant (production host): SHuffle T7 / References: UniProt: A0A6P5Y2I1
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 719 / 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: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 100 mM sodium acetate, 8% 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: Dec 12, 2021
RadiationMonochromator: C9111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.95→29.99 Å / Num. obs: 70433 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 32.64 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.033 / Rrim(I) all: 0.089 / Χ2: 0.93 / Net I/σ(I): 13.7
Reflection shellResolution: 1.95→1.99 Å / Rmerge(I) obs: 1.021 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4456 / CC1/2: 0.825 / Rpim(I) all: 0.399 / Rrim(I) all: 1.097 / Χ2: 0.89 / % 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: 1.95→29.99 Å / SU ML: 0.2047 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1257
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2195 3484 4.95 %
Rwork0.1789 66834 -
obs0.1809 70318 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.07 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5795 0 80 719 6594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086052
X-RAY DIFFRACTIONf_angle_d0.97918214
X-RAY DIFFRACTIONf_chiral_restr0.0662881
X-RAY DIFFRACTIONf_plane_restr0.00881068
X-RAY DIFFRACTIONf_dihedral_angle_d15.79492187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.3181410.25232627X-RAY DIFFRACTION99.86
1.98-20.28741470.24452623X-RAY DIFFRACTION99.93
2-2.030.28271360.23332603X-RAY DIFFRACTION99.78
2.03-2.070.27051480.22792669X-RAY DIFFRACTION99.96
2.07-2.10.27581090.20812636X-RAY DIFFRACTION99.89
2.1-2.140.25721440.2122659X-RAY DIFFRACTION99.96
2.14-2.180.26241220.20192627X-RAY DIFFRACTION99.85
2.18-2.220.24781350.20112646X-RAY DIFFRACTION99.96
2.22-2.260.24081350.2032660X-RAY DIFFRACTION99.82
2.26-2.310.23751470.1992635X-RAY DIFFRACTION99.86
2.31-2.370.27131390.2022665X-RAY DIFFRACTION99.93
2.37-2.420.24671180.19862688X-RAY DIFFRACTION100
2.42-2.490.26711270.19542631X-RAY DIFFRACTION99.93
2.49-2.560.24821320.19282667X-RAY DIFFRACTION99.86
2.56-2.650.22511490.1972662X-RAY DIFFRACTION100
2.65-2.740.23781630.19352639X-RAY DIFFRACTION99.93
2.74-2.850.25421230.19832686X-RAY DIFFRACTION99.96
2.85-2.980.24581410.18742661X-RAY DIFFRACTION99.96
2.98-3.140.23931460.18552687X-RAY DIFFRACTION99.96
3.14-3.330.23131390.18082710X-RAY DIFFRACTION99.93
3.33-3.590.21251610.17312656X-RAY DIFFRACTION99.89
3.59-3.950.21311490.16242708X-RAY DIFFRACTION99.93
3.95-4.520.16991380.14152726X-RAY DIFFRACTION99.93
4.52-5.690.17051470.14252762X-RAY DIFFRACTION99.9
5.69-29.990.19081480.17872901X-RAY DIFFRACTION99.74

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