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- PDB-8we5: Durio zibethinus trypsin inhibitor DzTI-6 -

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Basic information

Entry
Database: PDB / ID: 8we5
TitleDurio zibethinus trypsin inhibitor DzTI-6
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 / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDeetanya, 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 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 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)87,36526
Polymers85,3394
Non-polymers2,02622
Water20,0691114
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)98.584, 99.456, 115.675
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: 21334.832 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: OR361618 / 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.: 22 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1114 / 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: 3.53 Å3/Da / Density % sol: 65.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM Tris, 30% PEG 6,000

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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: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.85→29.95 Å / Num. obs: 97533 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 21.76 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.043 / Rrim(I) all: 0.116 / Χ2: 0.75 / Net I/σ(I): 13.5
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.856 / Mean I/σ(I) obs: 2 / Num. unique obs: 4761 / CC1/2: 0.798 / Rpim(I) all: 0.339 / Rrim(I) all: 0.921 / Χ2: 0.46 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSJan 10, 2022 BUILT=20220110data reduction
Aimless0.7.7data scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→29.11 Å / SU ML: 0.1819 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.4625
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1811 4735 4.86 %
Rwork0.1533 92703 -
obs0.1546 97438 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.5 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5644 0 132 1114 6890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00726135
X-RAY DIFFRACTIONf_angle_d0.87178356
X-RAY DIFFRACTIONf_chiral_restr0.0649893
X-RAY DIFFRACTIONf_plane_restr0.00881092
X-RAY DIFFRACTIONf_dihedral_angle_d14.5292210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.2851500.24453079X-RAY DIFFRACTION100
1.87-1.890.24991730.22083016X-RAY DIFFRACTION100
1.89-1.920.21921620.19813046X-RAY DIFFRACTION100
1.92-1.940.20051840.19032999X-RAY DIFFRACTION100
1.94-1.970.20271500.17673083X-RAY DIFFRACTION99.94
1.97-1.990.19391440.17133079X-RAY DIFFRACTION100
1.99-2.020.19811750.16683034X-RAY DIFFRACTION100
2.02-2.050.19231200.16743080X-RAY DIFFRACTION100
2.05-2.080.20931590.1613068X-RAY DIFFRACTION99.97
2.08-2.120.19931470.16473090X-RAY DIFFRACTION100
2.12-2.150.20441590.15763038X-RAY DIFFRACTION100
2.15-2.190.19471630.1573076X-RAY DIFFRACTION100
2.19-2.240.1731290.15833091X-RAY DIFFRACTION100
2.24-2.280.17811440.15473065X-RAY DIFFRACTION100
2.28-2.330.19791540.15653096X-RAY DIFFRACTION100
2.33-2.380.19941860.16413028X-RAY DIFFRACTION99.97
2.38-2.440.2071720.16413058X-RAY DIFFRACTION99.97
2.44-2.510.20751450.16713086X-RAY DIFFRACTION99.97
2.51-2.580.231450.16843102X-RAY DIFFRACTION99.97
2.58-2.670.21071520.163112X-RAY DIFFRACTION100
2.67-2.760.18481760.15973081X-RAY DIFFRACTION100
2.76-2.870.17741630.15523072X-RAY DIFFRACTION100
2.87-30.1951590.15383090X-RAY DIFFRACTION100
3-3.160.18061560.15133110X-RAY DIFFRACTION100
3.16-3.360.16421420.14643116X-RAY DIFFRACTION99.97
3.36-3.620.15161890.12863108X-RAY DIFFRACTION100
3.62-3.980.14771580.12493139X-RAY DIFFRACTION100
3.98-4.560.13851700.11793134X-RAY DIFFRACTION100
4.56-5.730.13291480.13483202X-RAY DIFFRACTION100
5.73-29.110.23221610.18113325X-RAY DIFFRACTION99.66

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