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- PDB-6kv2: Crystal structure of trypsin inhibitor 1 from Senna obtusifolia -

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Basic information

Entry
Database: PDB / ID: 6kv2
TitleCrystal structure of trypsin inhibitor 1 from Senna obtusifolia
ComponentsTrypsin inhibitor 1
KeywordsOXIDOREDUCTASE / trypsin inhibitor
Function / homologyoxalate oxidase / oxalate oxidase activity / Soybean 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 / serine-type endopeptidase inhibitor activity / Trypsin inhibitor 1
Function and homology information
Biological speciesSenna obtusifolia (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.003 Å
AuthorsLiao, H. / Yu, Y.
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Structural and functional relationship of Cassia obtusifolia trypsin inhibitor to understand its digestive resistance against Pieris rapae.
Authors: Zhou, J. / Li, C. / Chen, A. / Zhu, J. / Zou, M. / Liao, H. / Yu, Y.
History
DepositionSep 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trypsin inhibitor 1
B: Trypsin inhibitor 1
D: Trypsin inhibitor 1
C: Trypsin inhibitor 1


Theoretical massNumber of molelcules
Total (without water)83,6884
Polymers83,6884
Non-polymers00
Water6,035335
1
A: Trypsin inhibitor 1


Theoretical massNumber of molelcules
Total (without water)20,9221
Polymers20,9221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Trypsin inhibitor 1


Theoretical massNumber of molelcules
Total (without water)20,9221
Polymers20,9221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Trypsin inhibitor 1


Theoretical massNumber of molelcules
Total (without water)20,9221
Polymers20,9221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Trypsin inhibitor 1


Theoretical massNumber of molelcules
Total (without water)20,9221
Polymers20,9221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.586, 84.753, 126.644
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Trypsin inhibitor 1


Mass: 20921.900 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Senna obtusifolia (plant) / Gene: TI1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A097P6E1*PLUS, oxalate oxidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.8M Ammonium Sulphate 0.1M Bis-Tris pH5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 55444 / % possible obs: 100 % / Redundancy: 11.9 % / Biso Wilson estimate: 33.94 Å2 / CC1/2: 0.989 / Net I/σ(I): 12.6
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 2675 / CC1/2: 0.618

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.003→47.603 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.8
RfactorNum. reflection% reflection
Rfree0.2211 971 2.05 %
Rwork0.186 --
obs0.1867 47419 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 163.95 Å2 / Biso mean: 39.73 Å2 / Biso min: 20.79 Å2
Refinement stepCycle: final / Resolution: 2.003→47.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5440 0 0 335 5775
Biso mean---40.37 -
Num. residues----710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035565
X-RAY DIFFRACTIONf_angle_d0.8257518
X-RAY DIFFRACTIONf_chiral_restr0.031825
X-RAY DIFFRACTIONf_plane_restr0.003975
X-RAY DIFFRACTIONf_dihedral_angle_d12.0152002
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.003-2.10850.28311510.2492643099
2.1085-2.24060.30381390.22596576100
2.2406-2.41360.25031340.20396581100
2.4136-2.65650.22341290.20286584100
2.6565-3.04080.21881490.19096632100
3.0408-3.83090.20891320.17076703100
3.8309-47.60.19761370.16976942100

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