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

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Basic information

Entry
Database: PDB / ID: 6yix
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
[azanyl(thiophen-3-yl)methylidene]azanium / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 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 1.1Jan 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 1.2Oct 23, 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

Downloads & links

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Assembly

Deposited unit
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9568
Polymers23,3241
Non-polymers6327
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-13 kcal/mol
Surface area8890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.366, 58.099, 66.654
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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
Details: ...Details: IVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRVASISLPTSCASAGTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDSCQGDSGGPVVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN
Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00760, trypsin
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-8M2 / [azanyl(thiophen-3-yl)methylidene]azanium


Mass: 127.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H7N2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.04 Å3/Da / Density % sol: 39.78 %
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: 1.31→50 Å / Num. obs: 50997 / % possible obs: 98.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 11.64 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.98
Reflection shellResolution: 1.31→1.39 Å / Redundancy: 4.6 % / Num. unique obs: 8098 / CC1/2: 0.841 / % possible all: 98.3

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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: 1.31→42.13 Å / SU ML: 0.1189 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.4284
RfactorNum. reflection% reflection
Rfree0.1935 2547 5 %
Rwork0.1768 --
obs0.1777 50987 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 13.51 Å2
Refinement stepCycle: LAST / Resolution: 1.31→42.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1615 0 34 210 1859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641755
X-RAY DIFFRACTIONf_angle_d0.95342393
X-RAY DIFFRACTIONf_chiral_restr0.0861263
X-RAY DIFFRACTIONf_plane_restr0.0069323
X-RAY DIFFRACTIONf_dihedral_angle_d12.0633637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.330.21761370.17212600X-RAY DIFFRACTION96.85
1.33-1.360.23221410.18052683X-RAY DIFFRACTION99.3
1.36-1.390.2491380.18162636X-RAY DIFFRACTION98.68
1.39-1.420.23581400.16622654X-RAY DIFFRACTION98.9
1.42-1.460.22271400.16822662X-RAY DIFFRACTION99.26
1.46-1.50.20241390.15372653X-RAY DIFFRACTION99.39
1.5-1.540.22961410.15112687X-RAY DIFFRACTION99.65
1.54-1.590.17751430.14922705X-RAY DIFFRACTION99.41
1.59-1.650.18351410.15482681X-RAY DIFFRACTION99.54
1.65-1.720.20511400.14342667X-RAY DIFFRACTION98.94
1.72-1.790.19011410.14942670X-RAY DIFFRACTION98.94
1.79-1.890.16561400.15752673X-RAY DIFFRACTION98.08
1.89-2.010.15871410.15772689X-RAY DIFFRACTION98.71
2.01-2.160.16621410.15542695X-RAY DIFFRACTION98.68
2.16-2.380.19471420.1652703X-RAY DIFFRACTION99.23
2.38-2.720.17351450.18522747X-RAY DIFFRACTION99.76
2.72-3.430.21221450.19432759X-RAY DIFFRACTION98.88
3.43-42.130.19521520.212876X-RAY DIFFRACTION98.66

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