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- PDB-2iln: Crystal structure of the Bowman-Birk inhibitor from snail medic s... -

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Basic information

Entry
Database: PDB / ID: 2iln
TitleCrystal structure of the Bowman-Birk inhibitor from snail medic seeds in complex with bovine trypsin
Components
  • Bowman-Birk type proteinase inhibitor
  • Cationic trypsin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Medicago scutellata / protease inhibitor / Bowman-Birk inhibitor / trypsin / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Cysteine Protease (Bromelain) Inhibitor, subunit H / Cysteine Protease (Bromelain) Inhibitor, subunit H / Bowman-Birk serine protease inhibitor family / Bowman-Birk serine protease inhibitors family signature. / Proteinase inhibitor I12, Bowman-Birk / Bowman-Birk type proteinase inhibitor / Bowman-Birk type proteinase inhibitor / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site ...Cysteine Protease (Bromelain) Inhibitor, subunit H / Cysteine Protease (Bromelain) Inhibitor, subunit H / Bowman-Birk serine protease inhibitor family / Bowman-Birk serine protease inhibitors family signature. / Proteinase inhibitor I12, Bowman-Birk / Bowman-Birk type proteinase inhibitor / Bowman-Birk type proteinase inhibitor / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Serine protease 1 / Bowman-Birk type proteinase inhibitor
Similarity search - Component
Biological speciesBos taurus (cattle)
Medicago scutellata (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCapaldi, S. / Perduca, M. / Faggion, B. / Carrizo, M.E. / Tava, A. / Ragona, L. / Monaco, H.L.
CitationJournal: J.Struct.Biol. / Year: 2007
Title: Crystal structure of the anticarcinogenic Bowman-Birk inhibitor from snail medic (Medicago scutellata) seeds complexed with bovine trypsin
Authors: Capaldi, S. / Perduca, M. / Faggion, B. / Carrizo, M.E. / Tava, A. / Ragona, L. / Monaco, H.L.
History
DepositionOct 3, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 25, 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

Downloads & links

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Assembly

Deposited unit
A: Cationic trypsin
B: Cationic trypsin
I: Bowman-Birk type proteinase inhibitor


Theoretical massNumber of molelcules
Total (without water)53,5893
Polymers53,5893
Non-polymers00
Water6,774376
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.470, 54.470, 180.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Cationic trypsin / Trypsinogen / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: pancreas / References: UniProt: P00760, trypsin
#2: Protein Bowman-Birk type proteinase inhibitor / MSTI


Mass: 6940.019 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Medicago scutellata (plant) / Tissue: seed / References: UniProt: P80321
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O

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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: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.5M lithium sulphate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 5, 2004 / Details: Mirrors: Three-segment Pt-coated toroidal
RadiationMonochromator: Double Crystal (Si111, Si220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 34060 / Num. obs: 33730 / % possible obs: 95.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Rsym value: 0.093 / Net I/σ(I): 4
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 2479 / Rsym value: 0.28 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D6R

1d6r


Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.909 / SU B: 6.702 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.242 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28686 1680 5 %RANDOM
Rwork0.23194 ---
all0.2348 31992 --
obs0.2348 31992 95.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.668 Å2
Baniso -1Baniso -2Baniso -3
1-2.38 Å20 Å20 Å2
2--2.38 Å20 Å2
3----4.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.211 Å0.242 Å
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3669 0 0 376 4045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223760
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.9485112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.435496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.59725.373134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79915605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.559158
X-RAY DIFFRACTIONr_chiral_restr0.0970.2569
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022801
X-RAY DIFFRACTIONr_nbd_refined0.2020.21792
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22551
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2362
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2490.213
X-RAY DIFFRACTIONr_mcbond_it0.5521.52514
X-RAY DIFFRACTIONr_mcangle_it0.96723965
X-RAY DIFFRACTIONr_scbond_it1.3731432
X-RAY DIFFRACTIONr_scangle_it2.134.51147
LS refinement shellResolution: 2.001→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 115 -
Rwork0.296 2380 -
obs-2495 97.23 %

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