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- PDB-8wq6: Durio zibethinus trypsin inhibitor DzTI-5 (lattice translocation ... -

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Basic information

Entry
Database: PDB / ID: 8wq6
TitleDurio zibethinus trypsin inhibitor DzTI-5 (lattice translocation disorder)
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: 1.55 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
DepositionOct 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 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

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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)44,86625
Polymers43,2152
Non-polymers1,65223
Water8,413467
1
A: 21 kDa seed protein-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,37913
Polymers21,6071
Non-polymers77212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-49 kcal/mol
Surface area9770 Å2
MethodPISA
2
B: 21 kDa seed protein-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,48712
Polymers21,6071
Non-polymers88011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-43 kcal/mol
Surface area9170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.933, 64.098, 128.341
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: 21607.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Durio zibethinus (durian) / Strain: Chanee / Gene: LOC111287662 / Plasmid: pET32b / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 / References: UniProt: A0A6P5Y0V4
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / 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.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.65 Å3/Da / Density % sol: 53.65 %
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→29.7 Å / Num. obs: 65419 / % possible obs: 100 % / Redundancy: 14.5 % / Biso Wilson estimate: 17.08 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.029 / Rrim(I) all: 0.11 / Χ2: 0.91 / Net I/σ(I): 14.4
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 14.1 % / Rmerge(I) obs: 1.578 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3188 / CC1/2: 0.837 / Rpim(I) all: 0.435 / Rrim(I) all: 1.638 / Χ2: 0.71 / % 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: 1.55→29.7 Å / SU ML: 0.1647 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.19
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2465 3215 4.93 %
Rwork0.2213 62016 -
obs0.2225 65231 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.49 Å2
Refinement stepCycle: LAST / Resolution: 1.55→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2939 0 50 467 3456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00623034
X-RAY DIFFRACTIONf_angle_d0.86784111
X-RAY DIFFRACTIONf_chiral_restr0.0575443
X-RAY DIFFRACTIONf_plane_restr0.0062533
X-RAY DIFFRACTIONf_dihedral_angle_d16.07611094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.2941430.27462621X-RAY DIFFRACTION99.93
1.57-1.60.29221520.27132665X-RAY DIFFRACTION99.79
1.6-1.620.28791220.25732660X-RAY DIFFRACTION99.75
1.62-1.650.34261350.24612677X-RAY DIFFRACTION99.93
1.65-1.680.27171110.23012696X-RAY DIFFRACTION99.96
1.68-1.710.25651700.23462617X-RAY DIFFRACTION99.93
1.71-1.750.25811260.21952699X-RAY DIFFRACTION99.75
1.75-1.790.24921370.22232674X-RAY DIFFRACTION99.72
1.79-1.830.23291400.21692651X-RAY DIFFRACTION99.75
1.83-1.870.24471580.21992648X-RAY DIFFRACTION99.64
1.87-1.930.26531160.21462688X-RAY DIFFRACTION99.82
1.93-1.980.23891310.2132678X-RAY DIFFRACTION99.79
1.98-2.050.23021540.21512691X-RAY DIFFRACTION99.68
2.05-2.120.27851490.21652645X-RAY DIFFRACTION99.68
2.12-2.20.22721440.2172708X-RAY DIFFRACTION99.79
2.2-2.30.23991330.21612680X-RAY DIFFRACTION99.65
2.3-2.430.25641320.22372721X-RAY DIFFRACTION99.93
2.43-2.580.26521420.23182709X-RAY DIFFRACTION99.86
2.58-2.780.28341530.2332697X-RAY DIFFRACTION99.72
2.78-3.060.22281190.22182757X-RAY DIFFRACTION99.93
3.06-3.50.22411430.20722756X-RAY DIFFRACTION100
3.5-4.40.24171450.20222780X-RAY DIFFRACTION100
4.4-29.70.22921600.23092898X-RAY DIFFRACTION99.64

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