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- PDB-6yiy: Trypsin inhibitor in complex with bovine trypsin -

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Basic information

Entry
Database: PDB / ID: 6yiy
TitleTrypsin inhibitor in complex with bovine trypsin
ComponentsCationic trypsin
KeywordsHYDROLASE / Fragment / protease / Serine protease
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / 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
1H-isoindol-3-amine / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.11 Å
AuthorsBadran, M.J. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Trypsin inhibitor in complex with bovine trypsin
Authors: Badran, M.J. / Heine, A. / Klebe, G.
History
DepositionApr 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 2.0Mar 3, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_seq_num
Revision 2.1Jan 24, 2024Group: 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
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8097
Polymers23,3241
Non-polymers4856
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-6 kcal/mol
Surface area8810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.609, 54.609, 107.517
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-579-

HOH

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Components

#1: Protein Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00760, trypsin
#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-F05 / 1H-isoindol-3-amine


Mass: 132.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8N2 / Feature type: SUBJECT OF INVESTIGATION
#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.: 185 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.81 Å3/Da / Density % sol: 32.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: ammonium sulfat, PEG8000, ethylene glycol, HEPES / PH range: 6.5 _ 7.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 29, 2019
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.11→50 Å / Num. obs: 73703 / % possible obs: 99.3 % / Redundancy: 6.47 % / Biso Wilson estimate: 12.04 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.98
Reflection shellResolution: 1.11→1.18 Å / Num. unique obs: 11641 / CC1/2: 0.848

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MNK

5mnk


Resolution: 1.11→47.29 Å / SU ML: 0.0792 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.2248
RfactorNum. reflection% reflection
Rfree0.1574 3686 5 %
Rwork0.1402 --
obs0.1411 73701 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 15.08 Å2
Refinement stepCycle: LAST / Resolution: 1.11→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1606 0 27 185 1818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00561750
X-RAY DIFFRACTIONf_angle_d0.93922394
X-RAY DIFFRACTIONf_chiral_restr0.0848269
X-RAY DIFFRACTIONf_plane_restr0.0064321
X-RAY DIFFRACTIONf_dihedral_angle_d11.5326633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.11-1.120.20871370.18852604X-RAY DIFFRACTION96.92
1.12-1.140.1851410.17252671X-RAY DIFFRACTION98.49
1.14-1.160.17051380.1642613X-RAY DIFFRACTION98.39
1.16-1.170.18811370.16492603X-RAY DIFFRACTION98.56
1.17-1.190.20071400.15252658X-RAY DIFFRACTION98.83
1.19-1.210.1791400.14822677X-RAY DIFFRACTION99.05
1.21-1.230.16611390.14242634X-RAY DIFFRACTION98.89
1.23-1.250.14931390.13522637X-RAY DIFFRACTION98.86
1.25-1.280.16631410.13952679X-RAY DIFFRACTION98.81
1.28-1.30.17071400.1352656X-RAY DIFFRACTION99.47
1.3-1.330.16371400.1282669X-RAY DIFFRACTION99.4
1.33-1.360.13921420.12652689X-RAY DIFFRACTION99.51
1.36-1.40.16291400.12732661X-RAY DIFFRACTION99.61
1.4-1.440.13131410.11992685X-RAY DIFFRACTION99.61
1.44-1.480.14141420.11322708X-RAY DIFFRACTION99.72
1.48-1.530.1351420.11462697X-RAY DIFFRACTION99.82
1.53-1.580.13091410.11292671X-RAY DIFFRACTION99.86
1.58-1.640.11651420.11352691X-RAY DIFFRACTION99.89
1.64-1.720.14461430.1142726X-RAY DIFFRACTION100
1.72-1.810.13621430.12082712X-RAY DIFFRACTION100
1.81-1.920.13931420.11772706X-RAY DIFFRACTION99.79
1.92-2.070.13691450.11792746X-RAY DIFFRACTION99.9
2.07-2.280.15661450.12372755X-RAY DIFFRACTION99.97
2.28-2.610.12851450.13182761X-RAY DIFFRACTION99.97
2.61-3.290.16851460.15062777X-RAY DIFFRACTION99.93
3.29-47.290.18751550.17712929X-RAY DIFFRACTION99.39

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