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- PDB-5xoz: Crystal structure of a Kunitz type trypsin inhibitor from Cicer a... -

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Basic information

Entry
Database: PDB / ID: 5xoz
TitleCrystal structure of a Kunitz type trypsin inhibitor from Cicer arietinumL
ComponentsTrypsin protein inhibitor 2
KeywordsHYDROLASE INHIBITOR / Kunitz / Inhibitor / Beta-trefoil
Function / homology
Function and homology information


endopeptidase inhibitor activity / extracellular region
Similarity search - Function
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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Kunitz-type trypsin inhibitor-like 2 protein-like precursor
Similarity search - Component
Biological speciesCicer arietinum (chickpea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBendre, A.D. / Suresh, C.G. / Ramasamy, S.
Funding support India, 1items
OrganizationGrant numberCountry
Counsil for Scientific and Industrial Research India
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2019
Title: Structural insights into the unique inhibitory mechanism of Kunitz type trypsin inhibitor from Cicer arietinum L.
Authors: Bendre, A.D. / Suresh, C.G. / Shanmugam, D. / Ramasamy, S.
History
DepositionMay 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Dec 12, 2018Group: Data collection / Database references / Category: citation / Item: _citation.page_last
Revision 1.3May 29, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trypsin protein inhibitor 2
B: Trypsin protein inhibitor 2


Theoretical massNumber of molelcules
Total (without water)48,8112
Polymers48,8112
Non-polymers00
Water00
1
A: Trypsin protein inhibitor 2


Theoretical massNumber of molelcules
Total (without water)24,4051
Polymers24,4051
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Trypsin protein inhibitor 2


Theoretical massNumber of molelcules
Total (without water)24,4051
Polymers24,4051
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.730, 88.220, 59.340
Angle α, β, γ (deg.)90.00, 108.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Trypsin protein inhibitor 2 / kunitz-type trypsin inhibitor-like 2 protein-like precursor


Mass: 24405.338 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cicer arietinum (chickpea) / Gene: tpi2, kpi1, LOC101496724 / Production host: Komagataella pastoris GS115 (fungus) / Strain (production host): GS115 / References: UniProt: Q9M3Z7

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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: 1.97 Å3/Da / Density % sol: 37.62 % / Description: Diamond shaped crystal
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1M sodium acetate pH 5, 1M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 12, 2016
RadiationMonochromator: Water-cooled DCM with Si(111) and Si(220) crystals
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.8→56.33 Å / Num. obs: 9350 / % possible obs: 99.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 12

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R8N

1r8n


Resolution: 2.8→56.33 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.895 / Cross valid method: THROUGHOUT / ESU R Free: 0.349 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22052 476 5.1 %RANDOM
Rwork0.19615 ---
obs0.19736 8854 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.791 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20.24 Å2
2--0.93 Å2-0 Å2
3----0.79 Å2
Refinement stepCycle: 1 / Resolution: 2.8→56.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2717 0 0 0 2717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192785
X-RAY DIFFRACTIONr_bond_other_d00.022594
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.9813776
X-RAY DIFFRACTIONr_angle_other_deg3.7536052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3285355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.98824.655116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67315453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6941512
X-RAY DIFFRACTIONr_chiral_restr0.0860.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213115
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02549
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4262.9791425
X-RAY DIFFRACTIONr_mcbond_other2.4252.9771424
X-RAY DIFFRACTIONr_mcangle_it3.714.4641777
X-RAY DIFFRACTIONr_mcangle_other3.7094.4651778
X-RAY DIFFRACTIONr_scbond_it2.4263.0851360
X-RAY DIFFRACTIONr_scbond_other2.4263.0851360
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7994.5532000
X-RAY DIFFRACTIONr_long_range_B_refined5.07733.9952810
X-RAY DIFFRACTIONr_long_range_B_other5.07634.0092811
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 38 -
Rwork0.283 635 -
obs--98.68 %

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