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- PDB-8win: Durio zibethinus trypsin inhibitor DzTI-12 -

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Basic information

Entry
Database: PDB / ID: 8win
TitleDurio zibethinus trypsin inhibitor DzTI-12
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 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 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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


Theoretical massNumber of molelcules
Total (without water)43,2492
Polymers43,2492
Non-polymers00
Water00
1
A: 21 kDa seed protein-like


Theoretical massNumber of molelcules
Total (without water)21,6241
Polymers21,6241
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 21 kDa seed protein-like


Theoretical massNumber of molelcules
Total (without water)21,6241
Polymers21,6241
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)197.571, 197.571, 91.137
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

#1: Protein 21 kDa seed protein-like


Mass: 21624.264 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: OR361616 / 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
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: 3.96 Å3/Da / Density % sol: 68.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 100 mM sodium acetate, 2 M NaCl

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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→29.74 Å / Num. obs: 13733 / % possible obs: 99.9 % / Redundancy: 11.2 % / Biso Wilson estimate: 95.82 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.035 / Rrim(I) all: 0.115 / Χ2: 0.98 / Net I/σ(I): 13.6
Reflection shellResolution: 3→3.18 Å / Redundancy: 11.4 % / Rmerge(I) obs: 1.287 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2202 / CC1/2: 0.865 / Rpim(I) all: 0.398 / Rrim(I) all: 1.347 / Χ2: 1.04 / % 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→29.74 Å / SU ML: 0.4366 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.5424
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2764 700 5.1 %
Rwork0.2393 13024 -
obs0.2412 13724 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 107.14 Å2
Refinement stepCycle: LAST / Resolution: 3→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2895 0 0 0 2895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00982971
X-RAY DIFFRACTIONf_angle_d1.3094037
X-RAY DIFFRACTIONf_chiral_restr0.0709430
X-RAY DIFFRACTIONf_plane_restr0.0096524
X-RAY DIFFRACTIONf_dihedral_angle_d15.88321063
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.230.4331450.39472569X-RAY DIFFRACTION99.78
3.23-3.560.36061080.33352611X-RAY DIFFRACTION99.96
3.56-4.070.33931490.27172590X-RAY DIFFRACTION100
4.07-5.120.23921380.22942605X-RAY DIFFRACTION100
5.12-29.740.24061600.18912649X-RAY DIFFRACTION99.96

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