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- PDB-4xoj: Structure of bovine trypsin in complex with analogues of sunflowe... -

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Basic information

Entry
Database: PDB / ID: 4xoj
TitleStructure of bovine trypsin in complex with analogues of sunflower inhibitor 1 (SFTI-1)
Components
  • Cationic trypsin
  • Trypsin inhibitor 1
KeywordsHYDROLASE / trypsin / SFTI / inhibitor / splicing / protease
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
AMMONIUM ION / 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: 0.91 Å
AuthorsGolik, P. / Malicki, S. / Grudnik, P. / Karna, N. / Debowski, D. / Legowska, A. / Wladyka, B. / Gitlin, A. / Brzozowski, K. / Dubin, G. / Rolka, K.
CitationJournal: Chembiochem / Year: 2015
Title: Investigation of Serine-Proteinase-Catalyzed Peptide Splicing in Analogues of Sunflower Trypsin Inhibitor 1 (SFTI-1).
Authors: Karna, N. / Legowska, A. / Malicki, S. / Debowski, D. / Golik, P. / Gitlin, A. / Grudnik, P. / Wladyka, B. / Brzozowski, K. / Dubin, G. / Rolka, K.
History
DepositionJan 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Aug 9, 2017Group: Data collection / Database references / Category: citation_author / diffrn_source
Item: _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 / _struct_conn.ptnr2_label_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cationic trypsin
B: Trypsin inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,88515
Polymers27,2272
Non-polymers65813
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-32 kcal/mol
Surface area9180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.390, 63.050, 69.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Cationic trypsin / Beta-trypsin


Mass: 25806.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00760, trypsin
#2: Protein/peptide Trypsin inhibitor 1 / SFTI-1


Mass: 1420.741 Da / Num. of mol.: 1 / Fragment: UNP residues 40-52 / Source method: obtained synthetically / Source: (synth.) Helianthus annuus (common sunflower) / References: UniProt: Q4GWU5

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Non-polymers , 6 types, 373 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: sodium acetate trihydrate, PEG 8000, ammonium sulphate
PH range: 4.3 - 4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.91→23.3 Å / Num. obs: 193298 / % possible obs: 98.6 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.043 / Rsym value: 0.033 / Net I/σ(I): 14.8
Reflection shellResolution: 0.91→0.96 Å / Redundancy: 4 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 2.4 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I8G backbone model

4i8g


Resolution: 0.91→46.6 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.983 / SU B: 0.305 / SU ML: 0.008 / Cross valid method: THROUGHOUT / ESU R: 0.011 / ESU R Free: 0.012 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.11426 9713 5 %RANDOM
Rwork0.10329 ---
obs0.10384 183491 98.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.861 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å2-0 Å20 Å2
2---0.09 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 0.91→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 38 360 2116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.021996
X-RAY DIFFRACTIONr_bond_other_d0.0060.021874
X-RAY DIFFRACTIONr_angle_refined_deg2.1281.9632721
X-RAY DIFFRACTIONr_angle_other_deg1.74934379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.4495.152297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.09425.69265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.83515331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.836153
X-RAY DIFFRACTIONr_chiral_restr0.1290.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212318
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02431
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_it5.551.041028
X-RAY DIFFRACTIONr_mcbond_other5.5471.0311027
X-RAY DIFFRACTIONr_mcangle_it5.6141.5351298
X-RAY DIFFRACTIONr_mcangle_other5.6171.5431299
X-RAY DIFFRACTIONr_scbond_it8.1761.195968
X-RAY DIFFRACTIONr_scbond_other8.1721.202969
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.7721.6791397
X-RAY DIFFRACTIONr_long_range_B_refined8.90110.6012637
X-RAY DIFFRACTIONr_long_range_B_other8.90610.6082632
X-RAY DIFFRACTIONr_rigid_bond_restr6.98433870
X-RAY DIFFRACTIONr_sphericity_free41.043585
X-RAY DIFFRACTIONr_sphericity_bonded18.14454111
LS refinement shellResolution: 0.908→0.932 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 719 -
Rwork0.225 13449 -
obs--98.38 %

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