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- PDB-1sfi: High resolution structure of a potent, cyclic protease inhibitor ... -

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Basic information

Entry
Database: PDB / ID: 1sfi
TitleHigh resolution structure of a potent, cyclic protease inhibitor from sunflower seeds
Components
  • TRYPSIN
  • Trypsin inhibitor 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / TRYPSIN INHIBITOR / CYCLIC PEPTIDE / PROTEASE / BOVINE-TRYPSIN / SERINE PROTEASE-INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of endopeptidase activity / endopeptidase inhibitor activity / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / protease binding / endopeptidase activity / serine-type endopeptidase activity ...negative regulation of endopeptidase activity / endopeptidase inhibitor activity / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / protease binding / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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
Trypsin inhibitor 1 / Serine protease 1 / Trypsin inhibitor 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Helianthus annuus (common sunflower)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLuckett, S. / Garcia, R.S. / Barker, J.J. / Konarev, A.V. / Shewry, P. / Clarke, A.R. / Brady, R.L.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: High-resolution structure of a potent, cyclic proteinase inhibitor from sunflower seeds.
Authors: Luckett, S. / Garcia, R.S. / Barker, J.J. / Konarev, A.V. / Shewry, P.R. / Clarke, A.R. / Brady, R.L.
History
DepositionDec 16, 1998Processing site: BNL
Revision 1.0Jul 9, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Nov 9, 2016Group: Structure summary
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRYPSIN
I: Trypsin inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1886
Polymers24,8602
Non-polymers3284
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-56 kcal/mol
Surface area9430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.610, 64.430, 70.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRYPSIN


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00760, trypsin
#2: Protein/peptide Trypsin inhibitor 1 / SFTI-1


Type: Polypeptide / Class: Trypsin inhibitor / Mass: 1535.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CYCLIC PEPTIDE / Source: (natural) Helianthus annuus (common sunflower) / Organ: SEED / Strain: SUNBRED 246 / Tissue: ENDOSPERM / References: UniProt: Q4GWU5, Trypsin inhibitor 1
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCYCLIC PEPTIDE BOUND TO ACTIVE SITE OF TRYPSIN NO 3'-TERMINAL RESIDUE, CYCLIC PEPTIDE
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: 2.75 Å3/Da / Density % sol: 54.8 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
20.3 Mammonium sulfate1drop
36 mMcalcium chloride1drop
40.1 MTris-HCl1drop
560 mMbenzamidine1drop
71.6-2.1 Mammonium sulfate1reservoir
80.05 MTris-HCl1reservoir
6DMF1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.448
DetectorDetector: IMAGE PLATE / Date: May 1, 1998 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.448 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. obs: 32839 / % possible obs: 96.7 % / Redundancy: 2.5 % / Biso Wilson estimate: 18.43 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 14
Reflection shellResolution: 1.65→1.78 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 3.8 / % possible all: 91
Reflection
*PLUS
Num. measured all: 82087
Reflection shell
*PLUS
% possible obs: 91 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TLD

1tld


Resolution: 1.65→20 Å / SU B: 1.67 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.09
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1672 5 %SHELLS
Rwork0.175 ---
obs-30710 96.7 %-
Displacement parametersBiso mean: 21.11 Å2
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1734 0 16 376 2126
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0360.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.32
X-RAY DIFFRACTIONp_mcangle_it1.7873
X-RAY DIFFRACTIONp_scbond_it1.8222
X-RAY DIFFRACTIONp_scangle_it2.563
X-RAY DIFFRACTIONp_plane_restr0.02620.03
X-RAY DIFFRACTIONp_chiral_restr0.1380.15
X-RAY DIFFRACTIONp_singtor_nbd0.1670.3
X-RAY DIFFRACTIONp_multtor_nbd0.2390.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.10.3
X-RAY DIFFRACTIONp_planar_tor4.77
X-RAY DIFFRACTIONp_staggered_tor12.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor20.120
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.46

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