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- PDB-2aih: 1H-NMR solution structure of a trypsin/chymotrypsin Bowman-Birk i... -

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Basic information

Entry
Database: PDB / ID: 2aih
Title1H-NMR solution structure of a trypsin/chymotrypsin Bowman-Birk inhibitor from Lens culinaris.
ComponentsBowman-Birk type protease inhibitor, LCTI
KeywordsHYDROLASE / trypsin/chymotrypsin Bowman-Birk inhibitor / two-strands beta-sheet
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / extracellular region
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 / Mainly Beta
Similarity search - Domain/homology
Bowman-Birk type proteinase inhibitor
Similarity search - Component
Biological speciesLens culinaris (lentil)
MethodSOLUTION NMR / simulated annealing, molecular dynamics matrix relaxation energy minimization
AuthorsRagg, E.M. / Galbusera, V. / Scarafoni, A. / Negri, A. / Tedeschi, G. / Consonni, A. / Sessa, F. / Duranti, M.
CitationJournal: Febs J. / Year: 2006
Title: Inhibitory properties and solution structure of a potent Bowman-Birk protease inhibitor from lentil (Lens culinaris, L) seeds.
Authors: Ragg, E.M. / Galbusera, V. / Scarafoni, A. / Negri, A. / Tedeschi, G. / Consonni, A. / Sessa, F. / Duranti, M.
History
DepositionJul 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE According to authors, the Glu at position 110 in the sequence database is missing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bowman-Birk type protease inhibitor, LCTI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,86112
Polymers7,4711
Non-polymers39011
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 52back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1closest to the average

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Components

#1: Protein Bowman-Birk type protease inhibitor, LCTI / Trypsin/chymotrypsin inhibitor


Mass: 7471.454 Da / Num. of mol.: 1 / Fragment: residues 43-109 / Source method: isolated from a natural source / Source: (natural) Lens culinaris (lentil) / Strain: Macrosperma group / Tissue: SeedsSeed / References: UniProt: Q8W4Y8
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
2212D TOCSY
3312D TOCSY
4412D TOCSY
5512D TOCSY
3622D TOCSY
3712D NOESY
381DQF-COSY
392DQF-COSY
NMR detailsText: NOESY experiments were performed at 298 K at three different mixing times (0.080s, 0.120s, 0.350s) for distance restraints calculations and cross-peak volume measurements

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM LCTI, unbuffered solution, 90% H2O, 10% D2O90% H2O/10% D2O
21 mM LCTI, unbuffered solution, 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
13 mM 3.0 ambient 288 K
23 mM 3.0 ambient 293 K
33 mM 3.0 ambient 298 K
43 mM 3.0 ambient 303 K
55 mM 4.2 ambient 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6collection
XwinNMR2.6processing
Sparky3.106Goddard, T.D. and Kneller, D.G.data analysis
X-PLOR3.1851Brunger, A.T.refinement
X-PLOR3.1851Brunger, A.T.iterative matrix relaxation
RefinementMethod: simulated annealing, molecular dynamics matrix relaxation energy minimization
Software ordinal: 1
Details: the structures are based on a total of 2745 restraints, of which 632 are NOE-derived distance constraints for the initial stage of Simulated Annealing, 2068 are NOESY-derived cross-peak ...Details: the structures are based on a total of 2745 restraints, of which 632 are NOE-derived distance constraints for the initial stage of Simulated Annealing, 2068 are NOESY-derived cross-peak volumes for final refinement, 29 vicinal coupling constants restraints, 16 distance restraints for hydrogen bond definitions; The chloride atoms at the end of each model were added during the refinement stage of restrained energy minimization to reduce overall charge. Positions are not experimentally determined but are a result of calculations
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 52 / Conformers submitted total number: 20

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